SMTL ID : 8fw6.1

Human Lactate Dehydrogenase A in Complex with Inhibitor CHK-336

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 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.29, A.30, V.31, D.52, V.53, I.54, K.57, T.95, A.96, G.97, R.99, I.116, F.119, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: YBO.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.252 Hydrogen bonds: A:G.29, A:A.30, A:V.31, A:V.53, A:K.57, A:K.57, A:G.97, A:V.136, A:N.138, A:N.138, A:S.161 Water bridges: A:G.32, A:R.99, A:N.113 Salt bridges: A:K.57, A:R.99 NAI.14: 24 residues within 4Å: Chain B: V.26, G.27, V.28, 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, S.161, L.165, H.193, T.248, I.252 Ligands: YBO.15 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.165, B:I.252, B:I.252 Hydrogen bonds: B:V.28, B:G.29, B:A.30, B:V.31, B:V.53, B:G.97, B:V.136, B:N.138, B:N.138, B:S.161 Water bridges: B:G.32 Salt bridges: B:R.99 NAI.23: 25 residues within 4Å: Chain C: V.26, G.29, A.30, V.31, D.52, V.53, I.54, K.57, T.95, A.96, G.97, R.99, I.116, F.119, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: YBO.24 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:I.252 Hydrogen bonds: C:G.29, C:A.30, C:V.31, C:V.53, C:K.57, C:K.57, C:G.97, C:V.136, C:N.138, C:N.138, C:S.161 Water bridges: C:G.32, C:Y.83, C:R.99, C:N.113 Salt bridges: C:K.57, C:R.99 NAI.36: 24 residues within 4Å: Chain D: V.26, G.27, V.28, 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, S.161, L.165, H.193, T.248, I.252 Ligands: YBO.37 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:L.165, D:I.252, D:I.252 Hydrogen bonds: D:V.28, D:G.29, 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.32, D:Y.83, D:Y.83 Salt bridges: D:R.99

4 x YBO: (2P)-2-{5-(cyclopropylmethyl)-3-(4-fluorophenyl)-4-[(3-fluoro-4-sulfamoylphenyl)methyl]-1H-pyrazol-1-yl}-1,3-thiazole-4-carboxylic acid

YBO.2: 21 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 Ligands: NAI.1, EDO.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:R.106, A:L.109, A:N.138, A:P.139, A:A.238, A:Y.239, A:I.242 Hydrogen bonds: A:N.138, A:D.141, A:I.142, A:E.192, A:E.192, A:T.248 Salt bridges: A:R.169, A:H.193 YBO.15: 20 residues within 4Å: Chain B: 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, A.238, Y.239, I.242, T.248, L.323 Ligands: NAI.14, EDO.21 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.109, B:N.138, B:A.238, B:Y.239 Hydrogen bonds: B:N.138, B:D.141, B:I.142, B:E.192, B:E.192, B:T.248, B:T.248 Salt bridges: B:R.169, B:H.193 YBO.24: 21 residues within 4Å: Chain C: 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 Ligands: NAI.23, EDO.25 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:R.106, C:L.109, C:N.138, C:P.139, C:A.238, C:Y.239, C:I.242 Hydrogen bonds: C:N.138, C:D.141, C:D.141, C:I.142, C:E.192 Salt bridges: C:R.169, C:H.193 YBO.37: 20 residues within 4Å: Chain D: 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, A.238, Y.239, I.242, T.248, L.323 Ligands: NAI.36, EDO.43 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.109, D:N.138, D:A.238, D:Y.239 Hydrogen bonds: D:N.138, D:D.141, D:D.141, D:I.142, D:E.192, D:T.248 Salt bridges: D:R.169, D:H.193

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

EDO.3: 4 residues within 4Å: Chain A: R.106, Y.239, I.242 Ligands: YBO.2 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: M.63, Q.66 Chain C: Y.172, E.176 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: A.87, N.88, K.126, Y.127, P.129 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: G.208, V.209, S.210 Chain B: S.202 Ligands: EDO.9 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: A.30, M.33, A.34, Y.247, S.249, W.250 Chain C: W.250 Ligands: EDO.29 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: N.21, K.90, K.132, M.264, Q.297 Chain D: N.21 Ligand excluded by PLIP EDO.9: 12 residues within 4Å: Chain A: S.202, G.203, N.205, G.208, S.210 Chain B: S.202, G.203, M.204, N.205, G.208, S.210 Ligands: EDO.6 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: Q.66, P.75, K.76, I.77, V.78 Chain C: Y.172, E.176 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: I.283, K.284, D.285, A.320, D.321 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: L.280, Y.281, K.305, V.306 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Chain A: K.149 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain B: A.30, M.33, A.34, Y.247, S.249, W.250 Chain D: W.250 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain B: L.40, M.41, D.43, F.71, L.72, R.73 Chain D: K.42 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: N.164, S.167, A.168, R.171, P.272 Chain D: L.70, F.71 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: Y.10, N.11, L.12 Chain C: K.155 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: R.106, Y.239 Ligands: YBO.15 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain B: Q.66, S.69, P.75, K.76, I.77 Chain D: Y.172, E.176 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain C: R.106, Y.239, I.242 Ligands: YBO.24 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain A: Y.172, E.176 Chain C: M.63, Q.66 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain C: A.87, N.88, K.126, Y.127, P.129 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain C: G.208, V.209, S.210 Chain D: S.202 Ligands: EDO.31 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain A: W.250 Chain C: A.30, M.33, A.34, Y.247, S.249, W.250 Ligands: EDO.7 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain B: N.21 Chain C: N.21, K.90, K.132, M.264, Q.297 Ligand excluded by PLIP EDO.31: 12 residues within 4Å: Chain C: S.202, G.203, N.205, G.208, S.210 Chain D: S.202, G.203, M.204, N.205, G.208, S.210 Ligands: EDO.28 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain A: Y.172, E.176 Chain C: Q.66, P.75, K.76, I.77, V.78 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain C: I.283, K.284, D.285, A.320, D.321 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain C: L.280, Y.281, K.305, V.306 Ligand excluded by PLIP EDO.35: 1 residues within 4Å: Chain C: K.149 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain B: W.250 Chain D: A.30, M.33, A.34, Y.247, S.249, W.250 Ligand excluded by PLIP EDO.40: 7 residues within 4Å: Chain B: K.42 Chain D: L.40, M.41, D.43, F.71, L.72, R.73 Ligand excluded by PLIP EDO.41: 7 residues within 4Å: Chain B: L.70, F.71 Chain D: N.164, S.167, A.168, R.171, P.272 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain A: K.155 Chain D: Y.10, N.11, L.12 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain D: R.106, Y.239 Ligands: YBO.37 Ligand excluded by PLIP EDO.44: 7 residues within 4Å: Chain B: Y.172, E.176 Chain D: Q.66, S.69, P.75, K.76, I.77 Ligand excluded by PLIP

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

PEG.16: 5 residues within 4Å: Chain B: E.240, L.244 Chain D: E.55, D.56, K.59 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.59 PEG.38: 5 residues within 4Å: Chain B: E.55, D.56, K.59 Chain D: E.240, L.244 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lowther, W.T. et al., Human Lactate Dehydrogenase A in complex with inhibitor CHK-336. To Be Published

Release Date

2024-01-24

Peptides

L-lactate dehydrogenase A chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

L-lactate dehydrogenase A chain

Related Entries With Identical Sequence