SMTL ID : 6sbu.2 (1 other biounit)

X-ray Structure of Human LDHA with an Allosteric Inhibitor (Compound 3)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

homo-tetramer

Ligands

4 x L5N: 4-[[4-[(5-chloranylthiophen-2-yl)carbonylamino]-1,3-bis(oxidanylidene)isoindol-2-yl]methyl]benzoic acid(Non-covalent)

L5N.1: 14 residues within 4Å: Chain A: K.59, M.62, Q.66, H.67, S.69, L.70, T.74, P.75, K.76, I.77 Chain B: R.169, Y.172, L.173, S.237 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Q.66, A:Q.66, A:T.74, B:Y.172, B:L.173 Hydrogen bonds: A:I.77, B:Y.172, B:Y.172 Salt bridges: A:K.59 pi-Cation interactions: A:H.67 L5N.3: 15 residues within 4Å: Chain A: R.169, Y.172, L.173, V.234, S.237 Chain B: K.59, M.62, Q.66, H.67, S.69, L.70, T.74, P.75, K.76, I.77 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.172, A:L.173, B:Q.66, B:Q.66, B:T.74 Hydrogen bonds: A:Y.172, B:I.77 Salt bridges: B:K.59 pi-Cation interactions: B:H.67 L5N.4: 14 residues within 4Å: Chain C: K.59, M.62, Q.66, H.67, S.69, L.70, T.74, P.75, K.76, I.77 Chain D: R.169, Y.172, L.173, S.237 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Q.66, C:T.74, D:Y.172 Hydrogen bonds: C:I.77 Water bridges: C:K.59, C:S.79 Salt bridges: C:K.59 pi-Cation interactions: C:H.67 L5N.5: 16 residues within 4Å: Chain C: R.169, Y.172, L.173, Q.233, V.234, S.237 Chain D: K.59, M.62, Q.66, H.67, S.69, L.70, T.74, P.75, K.76, I.77 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Q.66, D:T.74, C:Y.172 Hydrogen bonds: D:I.77 Salt bridges: D:K.59 pi-Cation interactions: D:H.67 Halogen bonds: C:Q.233

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

NAI.2: 21 residues within 4Å: Chain A: G.29, A.30, V.31, D.52, V.53, I.54, Y.83, T.95, A.96, G.97, R.99, I.116, F.119, I.120, V.136, S.137, N.138, S.161, H.193, T.248, I.252 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.248, A:I.252 Hydrogen bonds: A:G.29, A:A.30, A:V.31, A:Y.83, A:T.95, A:G.97, A:N.138, A:N.138, A:S.161, A:H.193 Salt bridges: A:R.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Friberg, A. et al., Structural Evidence for Isoform-Selective Allosteric Inhibition of Lactate Dehydrogenase A. Acs Omega (2020)

Release Date

2020-06-10

Peptides

L-lactate dehydrogenase A chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

L-lactate dehydrogenase A chain

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