SMTL ID : 7m2n.1

Crystal structure of Human Lactate Dehydrogenase A with Inhibitor Compound 15

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 25 residues within 4Å: Chain A: V.26, G.27, G.29, A.30, V.31, D.52, V.53, I.54, T.95, A.96, G.97, R.99, I.116, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: EDO.14, YOJ.20 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.252, A:I.252 Hydrogen bonds: A:G.29, A:V.31, A:V.53, A:G.97, A:V.136, A:N.138, A:N.138, A:S.161 Water bridges: A:A.30, A:A.30, A:G.32, A:R.99 Salt bridges: A:R.99 NAI.32: 26 residues within 4Å: Chain B: V.26, G.27, V.28, G.29, A.30, V.31, D.52, V.53, I.54, K.57, T.95, A.96, G.97, R.99, I.116, I.120, V.136, S.137, N.138, S.161, L.165, H.193, T.248, I.252 Ligands: YOJ.50, EDO.52 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.252 Hydrogen bonds: B:V.28, B:A.30, B:V.31, B:V.53, B:K.57, B:K.57, B:G.97, B:V.136, B:N.138, B:N.138, B:S.161 Water bridges: B:G.29, B:G.32, B:G.97, B:A.98, B:R.99, B:N.138 Salt bridges: B:K.57, B:R.99 NAI.62: 24 residues within 4Å: Chain C: V.26, G.27, G.29, A.30, V.31, D.52, V.53, I.54, K.57, T.95, A.96, G.97, R.99, I.116, I.120, V.136, S.137, N.138, S.161, H.193, T.248, I.252 Ligands: EDO.67, YOJ.79 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:I.252 Hydrogen bonds: C:V.28, C:G.29, C:A.30, C:V.31, C:V.53, C:K.57, C:G.97, C:V.136, C:N.138, C:N.138, C:S.161 Water bridges: C:G.32 Salt bridges: C:K.57, C:R.99 NAI.92: 25 residues within 4Å: Chain D: V.26, G.27, G.29, A.30, V.31, D.52, V.53, I.54, K.57, T.95, A.96, G.97, R.99, I.116, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: YOJ.102 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.252 Hydrogen bonds: D:A.30, D:V.31, D:V.53, D:G.97, D:V.136, D:N.138, D:N.138, D:S.161 Water bridges: D:G.29, D:G.32, D:R.99 Salt bridges: D:R.99

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 8 residues within 4Å: Chain A: L.183, S.184, H.186 Chain C: R.171, H.186 Ligands: SO4.27, EDO.66, GOL.77 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Water bridges: A:S.184, A:A.207, C:R.269, C:V.270 Salt bridges: A:H.186, C:R.171, C:H.186 SO4.23: 4 residues within 4Å: Chain A: L.214, H.215, P.216 Chain B: Q.7 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.7 Salt bridges: A:H.215 SO4.27: 7 residues within 4Å: Chain A: R.171, H.186 Chain C: S.184, H.186 Ligands: SO4.2, EDO.11, EDO.21 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A Water bridges: C:S.184, C:A.207, A:R.171, A:R.269 Salt bridges: C:H.186, A:R.171, A:H.186 SO4.30: 2 residues within 4Å: Chain B: S.105, R.106 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.106 Salt bridges: B:R.106 SO4.31: 2 residues within 4Å: Chain B: N.108, R.112 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.108, B:N.108 Salt bridges: B:R.112 SO4.36: 8 residues within 4Å: Chain B: R.171, H.186 Chain D: L.183, S.184, H.186 Ligands: GOL.54, EDO.56, SO4.82 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:L.183 Water bridges: D:A.207, B:R.171, B:H.186 Salt bridges: D:H.186, B:R.171, B:H.186 SO4.47: 3 residues within 4Å: Chain B: K.118, Q.331, H.333 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.331 Salt bridges: B:K.118, B:H.333 SO4.60: 1 residues within 4Å: Chain C: K.328 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.328 SO4.82: 7 residues within 4Å: Chain B: L.183, S.184, H.186 Chain D: R.171, H.186 Ligands: SO4.36, EDO.95 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain B Water bridges: D:R.171, D:H.186, D:V.270, B:A.207 Salt bridges: D:R.171, D:H.186, B:H.186 SO4.104: 3 residues within 4Å: Chain D: S.105, R.106 Ligands: YOJ.102 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.106 Salt bridges: D:R.106

75 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 2 residues within 4Å: Chain A: Y.239 Ligands: YOJ.20 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: Q.66, P.75, K.76, I.77 Chain B: Y.172, E.176 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: W.148, K.149, G.152, F.153 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: R.177, E.229, V.230 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: L.40, M.41, D.43, F.71, L.72, R.73 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: E.55, K.59 Ligands: EDO.22 Ligand excluded by PLIP EDO.11: 10 residues within 4Å: Chain A: N.164, S.167, R.171, W.188, V.270, H.271, P.272 Chain B: L.70 Ligands: EDO.21, SO4.27 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain A: S.202, G.203, N.205, G.208, S.210 Chain C: S.202, G.203, G.208 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Chain A: T.3 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: A.98, N.113, N.138 Ligands: NAI.1, YOJ.20 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: W.148, P.154, K.155 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain A: K.149, G.152 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: N.88, S.128, P.129, N.130, C.131 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain A: Q.20, N.21, K.90, I.263, M.264, Q.297 Chain D: Q.20 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain A: L.183, D.258, R.269, H.271 Chain B: L.70, F.71 Ligands: EDO.11, SO4.27 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: E.55, G.80, K.81, D.82 Ligands: EDO.8 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain A: K.243, K.245 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: Y.172, G.175, E.176, V.180, P.182 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain A: A.30, Y.247 Chain B: Y.247 Ligands: EDO.45 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain B: E.329 Ligands: YOJ.50 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain B: L.40, M.41, D.43, F.71, L.72, R.73 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain B: V.53, I.54, E.55, D.56 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain B: Q.20, N.21, K.90, M.264 Chain C: Q.20, N.21 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain B: M.62, V.78, S.79 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain B: Y.145, W.324, Q.327, L.330, F.332, H.334 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain B: E.236, E.240, K.243 Ligand excluded by PLIP EDO.41: 1 residues within 4Å: Chain B: R.268 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain B: L.280, Y.281, K.305 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain B: T.220, D.221, K.222, K.228 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain B: P.154, N.156, R.157 Chain C: E.15 Ligand excluded by PLIP EDO.45: 8 residues within 4Å: Chain A: W.250 Chain B: A.30, M.33, A.34, Y.247, S.249, W.250 Ligands: EDO.26 Ligand excluded by PLIP EDO.46: 2 residues within 4Å: Chain B: H.333, H.334 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain B: E.55, D.56, K.59 Ligand excluded by PLIP EDO.49: 2 residues within 4Å: Chain B: W.324, K.328 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain B: V.53 Ligands: NAI.32, EDO.53 Ligand excluded by PLIP EDO.53: 5 residues within 4Å: Chain B: A.98, R.99, Q.101, R.112 Ligands: EDO.52 Ligand excluded by PLIP EDO.55: 3 residues within 4Å: Chain B: L.173, E.176, R.177 Ligand excluded by PLIP EDO.56: 7 residues within 4Å: Chain A: L.70 Chain B: L.183, D.258, R.269, H.271 Ligands: SO4.36, GOL.54 Ligand excluded by PLIP EDO.58: 4 residues within 4Å: Chain B: P.19, Q.20, K.90 Chain C: Q.20 Ligand excluded by PLIP EDO.59: 3 residues within 4Å: Chain B: D.6, Y.10 Chain C: K.305 Ligand excluded by PLIP EDO.61: 3 residues within 4Å: Chain C: P.154, N.156, R.157 Ligand excluded by PLIP EDO.63: 6 residues within 4Å: Chain C: Q.66, P.75, K.76, I.77 Chain D: Y.172, E.176 Ligand excluded by PLIP EDO.64: 4 residues within 4Å: Chain C: R.177, E.229, V.230, Q.233 Ligand excluded by PLIP EDO.65: 6 residues within 4Å: Chain C: L.40, M.41, D.43, F.71, L.72, R.73 Ligand excluded by PLIP EDO.66: 9 residues within 4Å: Chain C: N.164, S.167, R.171, W.188, V.270, P.272 Chain D: L.70 Ligands: SO4.2, GOL.77 Ligand excluded by PLIP EDO.67: 3 residues within 4Å: Chain C: A.98, R.99 Ligands: NAI.62 Ligand excluded by PLIP EDO.68: 3 residues within 4Å: Chain C: W.148, P.154, K.155 Ligand excluded by PLIP EDO.69: 2 residues within 4Å: Chain C: D.223, K.224 Ligand excluded by PLIP EDO.70: 4 residues within 4Å: Chain C: E.192, S.196, S.319, T.322 Ligand excluded by PLIP EDO.71: 5 residues within 4Å: Chain C: P.199, W.201, K.228, H.231, R.315 Ligand excluded by PLIP EDO.72: 4 residues within 4Å: Chain C: T.220, D.221, K.222, K.228 Ligand excluded by PLIP EDO.73: 2 residues within 4Å: Chain C: T.309, S.310 Ligand excluded by PLIP EDO.74: 2 residues within 4Å: Chain C: E.240 Chain D: K.59 Ligand excluded by PLIP EDO.75: 3 residues within 4Å: Chain C: Y.239 Ligands: GOL.78, EDO.80 Ligand excluded by PLIP EDO.76: 2 residues within 4Å: Chain C: W.324, K.328 Ligand excluded by PLIP EDO.80: 3 residues within 4Å: Chain C: K.243 Ligands: EDO.75, GOL.78 Ligand excluded by PLIP EDO.83: 6 residues within 4Å: Chain A: L.267, R.268 Chain C: G.179, V.180, H.181 Chain D: P.75 Ligand excluded by PLIP EDO.84: 5 residues within 4Å: Chain B: S.202, G.208 Chain D: S.202, G.208, S.210 Ligand excluded by PLIP EDO.85: 4 residues within 4Å: Chain D: R.177, E.229, V.230, Q.233 Ligand excluded by PLIP EDO.86: 6 residues within 4Å: Chain D: E.55, L.58, K.59, M.62, S.79, G.80 Ligand excluded by PLIP EDO.87: 3 residues within 4Å: Chain D: G.80, K.81, D.82 Ligand excluded by PLIP EDO.88: 3 residues within 4Å: Chain D: A.98, R.99, R.112 Ligand excluded by PLIP EDO.89: 2 residues within 4Å: Chain D: K.57, R.99 Ligand excluded by PLIP EDO.91: 5 residues within 4Å: Chain D: L.40, M.41, D.43, F.71, R.73 Ligand excluded by PLIP EDO.93: 5 residues within 4Å: Chain A: P.75 Chain B: H.181 Chain D: N.266, L.267, R.268 Ligand excluded by PLIP EDO.94: 7 residues within 4Å: Chain D: N.266, R.268, G.296, Q.297, N.298, G.299, S.301 Ligand excluded by PLIP EDO.95: 8 residues within 4Å: Chain C: L.70 Chain D: S.167, R.171, W.188, V.270, P.272 Ligands: SO4.82, EDO.105 Ligand excluded by PLIP EDO.96: 2 residues within 4Å: Chain D: Y.10, N.11 Ligand excluded by PLIP EDO.97: 3 residues within 4Å: Chain D: W.148, P.154, K.155 Ligand excluded by PLIP EDO.98: 2 residues within 4Å: Chain D: T.309, S.310 Ligand excluded by PLIP EDO.99: 3 residues within 4Å: Chain D: E.236, E.240, K.243 Ligand excluded by PLIP EDO.100: 3 residues within 4Å: Chain D: P.122, N.123, K.126 Ligand excluded by PLIP EDO.101: 2 residues within 4Å: Chain D: W.324, K.328 Ligand excluded by PLIP EDO.103: 2 residues within 4Å: Chain D: Y.239 Ligands: YOJ.102 Ligand excluded by PLIP EDO.105: 5 residues within 4Å: Chain D: L.183, D.258, R.269, H.271 Ligands: EDO.95 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 2 residues within 4Å: Chain A: K.126, Y.127 No protein-ligand interaction detected (PLIP) GOL.54: 10 residues within 4Å: Chain A: L.70 Chain B: N.164, S.167, R.171, W.188, V.270, H.271, P.272 Ligands: SO4.36, EDO.56 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.164, B:R.171, B:V.270 Water bridges: B:R.171, B:G.187 GOL.77: 7 residues within 4Å: Chain C: L.183, D.258, R.269, H.271 Chain D: L.70 Ligands: SO4.2, EDO.66 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Water bridges: A:L.183, D:R.73, B:R.73 Hydrogen bonds: C:R.269, C:H.271 GOL.78: 6 residues within 4Å: Chain C: E.236, Y.239, E.240, K.243 Ligands: EDO.75, EDO.80 No protein-ligand interaction detected (PLIP) GOL.81: 3 residues within 4Å: Chain C: Y.239, I.242 Ligands: YOJ.79 No protein-ligand interaction detected (PLIP) GOL.90: 4 residues within 4Å: Chain D: Q.101, E.104, N.108, R.112 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.101, D:N.108

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 3 residues within 4Å: Chain A: K.149, Q.331, F.332 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.149, A:K.149, A:F.332 PEG.17: 8 residues within 4Å: Chain A: V.198, P.199, W.201, K.228, H.231, E.311, E.312, R.315 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.228, A:E.312, A:R.315 PEG.28: 4 residues within 4Å: Chain A: M.41, D.43 Chain D: M.41, D.43 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:M.41, A:M.41 PEG.40: 5 residues within 4Å: Chain B: Q.100, R.106, Y.239, I.242 Ligands: YOJ.50 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.100, B:R.106, B:Y.239 PEG.51: 2 residues within 4Å: Chain B: T.309, S.310 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.310 PEG.57: 4 residues within 4Å: Chain B: Q.20 Chain C: K.90, K.132, Q.297 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.132, C:I.263

4 x YOJ: 5-[(5'-{1-(4-carboxy-1,3-thiazol-2-yl)-5-(cyclopropylmethyl)-4-[(3-fluoro-4-sulfamoylphenyl)methyl]-1H-pyrazol-3-yl}-2'-fluoro[1,1'-biphenyl]-4-yl)oxy]-1H-1,2,3-triazole-4-carboxylic acid(Non-covalent)

YOJ.20: 23 residues within 4Å: Chain A: R.106, L.109, V.110, N.138, P.139, V.140, D.141, I.142, L.165, R.169, E.192, H.193, G.194, D.195, A.238, Y.239, I.242, T.248, L.323, I.326 Ligands: NAI.1, EDO.3, EDO.14 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.109, A:V.110, A:N.138, A:A.238, A:Y.239 Hydrogen bonds: A:R.106, A:N.138, A:D.141, A:I.142, A:E.192, A:E.192, A:T.248 Water bridges: A:R.106, A:R.106 Salt bridges: A:R.169, A:H.193 Halogen bonds: A:R.106 YOJ.50: 24 residues within 4Å: Chain B: R.106, L.107, L.109, V.110, N.138, P.139, V.140, D.141, I.142, L.165, R.169, E.192, H.193, G.194, D.195, A.238, Y.239, I.242, T.248, L.323, I.326 Ligands: EDO.29, NAI.32, PEG.40 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:R.106, B:L.109, B:V.110, B:N.138, B:A.238, B:Y.239 Hydrogen bonds: B:N.138, B:D.141, B:D.141, B:I.142, B:E.192 Salt bridges: B:R.169, B:H.193 YOJ.79: 23 residues within 4Å: Chain C: R.106, L.107, L.109, V.110, N.138, P.139, V.140, D.141, I.142, L.165, R.169, E.192, H.193, G.194, D.195, A.238, Y.239, I.242, T.248, L.323, I.326 Ligands: NAI.62, GOL.81 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:L.109, C:V.110, C:N.138, C:P.139, C:A.238, C:Y.239 Hydrogen bonds: C:N.138, C:D.141, C:D.141, C:I.142, C:E.192, C:E.192, C:T.248 Salt bridges: C:R.169, C:H.193 YOJ.102: 24 residues within 4Å: Chain D: R.106, L.107, L.109, V.110, N.138, P.139, V.140, D.141, I.142, L.165, R.169, E.192, H.193, G.194, D.195, A.238, Y.239, I.242, T.248, L.323, I.326 Ligands: NAI.92, EDO.103, SO4.104 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:L.109, D:V.110, D:N.138, D:P.139, D:A.238, D:Y.239 Hydrogen bonds: D:L.107, D:N.138, D:D.141, D:I.142, D:E.192 Salt bridges: D:R.106, D:R.169, D:H.193 Halogen bonds: D:R.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ding, J. et al., Dual Glycolate Oxidase/Lactate Dehydrogenase A Inhibitors for Primary Hyperoxaluria. ACS Medicinal Chemistry Letters (2021)

Release Date

2021-07-14

Peptides

L-lactate dehydrogenase A chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-lactate dehydrogenase A chain

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