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

X-ray Structure of Human LDH-A with an Allosteric Inhibitor (Compound 7)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

4 x L5K: ~{N}-[3-[(7-nitrodibenzofuran-2-yl)sulfonylamino]phenyl]-1-oxidanyl-cyclopropane-1-carboxamide(Non-covalent)

L5K.1: 19 residues within 4Å: Chain A: R.169, Y.172, L.173, G.175, E.176, G.179, V.180, H.181, P.182, Q.233, S.237 Chain B: Q.66, H.67, S.69, L.70, T.74, P.75, K.76, I.77 12 PLIP interactions: 1 interactions with chain C, 5 interactions with chain B, 6 interactions with chain A Water bridges: C:R.268 Hydrophobic interactions: B:L.70, B:T.74, A:Y.172, A:Y.172, A:Y.172 Hydrogen bonds: B:Q.66, B:P.75, B:I.77, A:Y.172 pi-Stacking: A:Y.172, A:Y.172 L5K.2: 17 residues within 4Å: Chain A: Q.66, H.67, S.69, L.70, T.74, P.75, K.76, I.77 Chain B: R.169, Y.172, L.173, E.176, G.179, V.180, H.181, Q.233, S.237 14 PLIP interactions: 6 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:L.70, A:T.74, B:Y.172, B:Y.172, B:Y.172, B:L.173 Hydrogen bonds: A:Q.66, A:P.75, A:I.77, B:Y.172 Water bridges: A:H.67, B:S.237 pi-Stacking: B:Y.172, B:Y.172 L5K.3: 17 residues within 4Å: Chain C: R.169, Y.172, L.173, G.175, E.176, V.180, H.181, Q.233, S.237 Chain D: Q.66, H.67, S.69, L.70, T.74, P.75, K.76, I.77 13 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: D:L.70, D:T.74, C:Y.172, C:Y.172, C:Y.172 Hydrogen bonds: D:Q.66, D:P.75, D:I.77, C:Y.172, C:Y.172 Water bridges: A:R.268 pi-Stacking: C:Y.172, C:Y.172 L5K.4: 18 residues within 4Å: Chain C: Q.66, H.67, S.69, L.70, T.74, P.75, K.76, I.77 Chain D: R.169, Y.172, L.173, G.175, E.176, G.179, V.180, H.181, Q.233, S.237 13 PLIP interactions: 6 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:Q.66, C:L.70, C:T.74, D:Y.172, D:Y.172, D:Y.172 Hydrogen bonds: C:Q.66, C:P.75, C:I.77, D:Y.172, D:Y.172 pi-Stacking: D:Y.172, D:Y.172

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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