SMTL ID : 6mv8.1

LDHA structure in complex with inhibitor 14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 21 residues within 4Å: Chain A: V.26, G.29, A.30, V.31, D.52, V.53, I.54, T.95, A.96, G.97, I.116, I.120, V.136, S.137, N.138, V.140, L.165, H.193, T.248, I.252 Ligands: D3S.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.31, A:I.252, A:I.252 Hydrogen bonds: A:V.28, A:A.30, A:V.31, A:V.53, A:G.97, A:V.136, A:N.138, A:N.138 Water bridges: A:G.29, A:G.32 NAI.5: 24 residues within 4Å: Chain B: V.26, G.29, A.30, V.31, D.52, V.53, I.54, K.57, T.95, A.96, G.97, A.98, R.99, I.116, I.120, V.136, S.137, N.138, S.161, L.165, H.193, T.248, I.252 Ligands: LAC.8 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:V.31, B:I.252, B:I.252, 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:K.57 Salt bridges: B:K.57, B:R.99, B:R.99 NAI.9: 20 residues within 4Å: Chain C: G.29, A.30, V.31, D.52, V.53, I.54, T.95, A.96, G.97, I.116, I.120, V.136, S.137, N.138, V.140, L.165, H.193, T.248, I.252 Ligands: D3S.12 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:V.31, C:V.136, C:I.252, C:I.252 Hydrogen bonds: C:G.29, C:A.30, C:V.31, C:V.53, C:G.97, C:V.136, C:N.138, C:N.138, C:S.161 Water bridges: C:G.32 NAI.13: 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, A.98, R.99, I.116, I.120, V.136, S.137, N.138, V.140, L.165, H.193, I.252 Ligands: D3S.14 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.165, D:I.252, D:I.252 Hydrogen bonds: D:V.28, D:A.30, D:V.31, D:V.53, D:G.97, D:R.99, D:V.136, D:N.138, D:N.138 Water bridges: D:G.29, D:G.32 Salt bridges: D:R.99, D:R.99

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 5 residues within 4Å: Chain A: W.148, G.152, F.153, P.154, K.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.155 Water bridges: A:N.156 EPE.6: 5 residues within 4Å: Chain B: W.148, G.152, F.153, P.154, K.155 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.155 Salt bridges: B:K.155 EPE.10: 5 residues within 4Å: Chain C: W.148, G.152, F.153, P.154, K.155 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.155

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

SO4.3: 5 residues within 4Å: Chain A: R.171, H.186 Chain C: L.183, S.184, H.186 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Water bridges: A:H.186, A:V.270, C:L.183, C:A.207 Salt bridges: A:R.171, A:H.186, C:H.186 SO4.7: 5 residues within 4Å: Chain B: R.171, H.186 Chain D: L.183, S.184, H.186 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain B Water bridges: D:A.207, B:R.171, B:R.171, B:R.171, B:R.171, B:H.186, B:R.269 Salt bridges: D:H.186, B:R.171, B:H.186 SO4.11: 5 residues within 4Å: Chain A: L.183, S.184, H.186 Chain C: R.171, H.186 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:L.183 Water bridges: A:A.207, C:R.171, C:V.270 Salt bridges: A:H.186, C:R.171, C:H.186 SO4.15: 5 residues within 4Å: Chain B: L.183, S.184, H.186 Chain D: R.171, H.186 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Water bridges: D:V.270, D:V.270, B:A.207 Salt bridges: D:R.171, D:H.186, B:H.186

3 x D3S: (6S)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(2-hydroxyphenyl)-6-phenyl-5,6-dihydro-2H-pyran-2-one(Non-covalent)

D3S.4: 15 residues within 4Å: Chain A: N.138, L.165, D.166, R.169, H.193, G.194, D.195, V.234, V.235, A.238, Y.239, I.242, Y.247, T.248 Ligands: NAI.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.235, A:A.238, A:A.238, A:I.242, A:I.242 Hydrogen bonds: A:N.138, A:H.193, A:T.248, A:T.248 Salt bridges: A:R.169 pi-Stacking: A:Y.239 D3S.12: 13 residues within 4Å: Chain C: N.138, D.166, R.169, H.193, G.194, D.195, V.234, V.235, A.238, Y.239, I.242, T.248 Ligands: NAI.9 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:V.235, C:A.238, C:A.238, C:I.242, C:I.242 Hydrogen bonds: C:N.138, C:H.193, C:T.248, C:T.248 Salt bridges: C:R.169 pi-Stacking: C:Y.239 D3S.14: 14 residues within 4Å: Chain D: R.99, N.138, D.166, R.169, H.193, G.194, D.195, V.234, V.235, A.238, Y.239, I.242, T.248 Ligands: NAI.13 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:R.99, D:A.238, D:A.238, D:I.242, D:I.242 Hydrogen bonds: D:N.138, D:H.193, D:T.248, D:T.248 Salt bridges: D:R.169 pi-Stacking: D:Y.239

1 x LAC: LACTIC ACID(Non-covalent)

LAC.8: 7 residues within 4Å: Chain B: N.138, L.165, R.169, H.193, A.238, T.248 Ligands: NAI.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.138, B:H.193, B:T.248, B:T.248 Water bridges: B:R.169 Salt bridges: B:R.169, B:H.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, B. et al., Structure-based Optimization of Potent, Cell-ActiveHydroxylactam Inhibitors of Lactate Dehydrogenase. To Be Published

Release Date

2019-10-30

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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