SMTL ID : 7dbj.1

Crystal structure of human LDHB in complex with NADH, oxamate, and AXKO-0046

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 24 residues within 4Å: Chain A: G.29, Q.30, V.31, D.52, V.53, L.54, T.95, A.96, G.97, V.98, R.99, N.113, V.116, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: OXM.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:V.31, A:V.136, A:I.252, A:I.252 Hydrogen bonds: A:Q.30, A:V.31, A:V.53, A:G.97, A:V.98, A:N.113, A:V.136, A:N.138, A:N.138, A:S.161 Water bridges: A:G.29, A:Q.30, A:G.32, A:R.99, A:Q.100 Salt bridges: A:R.99, A:R.99 NAI.4: 26 residues within 4Å: Chain B: G.27, V.28, G.29, Q.30, V.31, D.52, V.53, L.54, T.95, A.96, G.97, V.98, R.99, L.109, N.113, V.116, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: OXM.5 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:V.31, B:I.252, B:I.252 Hydrogen bonds: B:V.28, B:G.29, B:Q.30, B:V.31, B:G.97, B:V.98, B:N.113, B:V.136, B:N.138, B:N.138, B:S.161 Water bridges: B:Q.30, B:G.32, B:R.99, B:Q.100 Salt bridges: B:R.99, B:R.99 NAI.8: 24 residues within 4Å: Chain C: G.29, Q.30, V.31, D.52, V.53, L.54, T.95, A.96, G.97, V.98, R.99, N.113, V.116, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: OXM.9 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:V.31, C:I.252 Hydrogen bonds: C:V.28, C:Q.30, C:V.31, C:V.53, C:G.97, C:V.98, C:N.113, C:V.136, C:N.138, C:N.138, C:S.161 Water bridges: C:G.29, C:Q.30, C:G.32, C:R.99, C:Q.100 Salt bridges: C:R.99, C:R.99 NAI.13: 24 residues within 4Å: Chain D: G.27, V.28, G.29, Q.30, V.31, D.52, V.53, L.54, T.95, A.96, G.97, V.98, R.99, N.113, V.116, V.136, S.137, N.138, S.161, L.165, H.193, T.248, I.252 Ligands: OXM.14 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:V.31, D:I.252 Hydrogen bonds: D:V.28, D:Q.30, D:V.31, D:G.97, D:V.98, D:N.113, D:V.136, D:N.138, D:N.138, D:S.161 Water bridges: D:G.29, D:Q.30, D:Q.30, D:G.32, D:V.53, D:R.99, D:Q.100 Salt bridges: D:R.99, D:R.99

4 x OXM: OXAMIC ACID(Non-covalent)

OXM.2: 9 residues within 4Å: Chain A: Q.100, R.106, N.138, L.165, R.169, H.193, A.238, T.248 Ligands: NAI.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.106, A:N.138, A:T.248, A:T.248, A:T.248 Water bridges: A:T.248 Salt bridges: A:R.106, A:R.169, A:H.193 OXM.5: 9 residues within 4Å: Chain B: Q.100, R.106, N.138, L.165, R.169, H.193, A.238, T.248 Ligands: NAI.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.106, B:N.138, B:T.248 Water bridges: B:T.248 Salt bridges: B:R.106, B:R.169, B:H.193 OXM.9: 9 residues within 4Å: Chain C: Q.100, R.106, N.138, L.165, R.169, H.193, A.238, T.248 Ligands: NAI.8 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:R.106, C:N.138, C:T.248, C:T.248, C:T.248 Water bridges: C:T.248 Salt bridges: C:R.106, C:R.169, C:H.193 OXM.14: 9 residues within 4Å: Chain D: Q.100, R.106, N.138, L.165, R.169, H.193, A.238, T.248 Ligands: NAI.13 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.106, D:N.138, D:T.248 Water bridges: D:T.248 Salt bridges: D:R.106, D:R.169, D:H.193

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

EDO.3: 7 residues within 4Å: Chain A: K.22, E.47, K.76, V.78, S.84, V.85, A.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.87 Water bridges: A:S.84 EDO.6: 6 residues within 4Å: Chain A: I.37, G.41 Chain B: I.37, S.38, G.41, L.254 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.38 EDO.10: 7 residues within 4Å: Chain C: I.283, E.284, N.285, V.287, K.317, D.321, W.324 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.282, C:E.284, C:N.285, C:K.317 EDO.11: 6 residues within 4Å: Chain C: I.37, G.41 Chain D: I.37, S.38, G.41, L.254 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.38 EDO.15: 4 residues within 4Å: Chain A: H.156 Chain D: A.12, E.13, E.14 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:H.156, D:E.13 EDO.16: 7 residues within 4Å: Chain D: V.198, A.199, W.201, G.219, H.231, E.312, Q.315 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.197, D:A.199, D:G.219, D:H.231 EDO.17: 4 residues within 4Å: Chain D: K.228, H.231, K.232, V.235 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.228, D:K.228, D:H.231 Water bridges: D:D.195, D:D.195, D:H.231

2 x H1U: N-[[3-[2-[(phenylmethyl)amino]ethyl]-1H-indol-2-yl]methyl]cycloheptanamine(Non-covalent)

H1U.7: 17 residues within 4Å: Chain A: S.202, G.203, N.205, G.208, S.210, E.213, K.307, L.308, K.309 Chain C: S.202, G.203, N.205, G.208, S.210, E.213, K.307, K.309 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:N.205, A:K.307, A:K.309, C:N.205, C:K.309 pi-Cation interactions: A:K.309 Hydrogen bonds: C:S.202, C:S.202, C:E.213 Water bridges: C:S.210 H1U.12: 17 residues within 4Å: Chain B: S.202, G.203, N.205, G.208, S.210, E.213, K.307, L.308, K.309 Chain D: S.202, G.203, N.205, G.208, S.210, E.213, K.307, K.309 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:N.205, D:K.309, D:K.309, B:N.205, B:K.307 Hydrogen bonds: D:S.202, D:S.202, D:E.213 Water bridges: D:S.210 pi-Cation interactions: B:K.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shibata, S. et al., Identification of the first highly selective inhibitor of human lactate dehydrogenase B. Sci Rep (2021)

Release Date

2021-10-20

Peptides

L-lactate dehydrogenase B chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-lactate dehydrogenase B chain

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