MolNFT v1 · #163740 · protein

X-ray structure of human ldh-a with an allosteric inhibitor (compound 7)

6SBV · L-lactate dehydrogenase a chain: “X-ray structure of human ldh-a with an allosteric inhibitor (compound 7)”. X-ray diffraction, 1 ligand (L5K), 20 pockets (best druggability 0.85). MolNFT v1 #163740 on GenesisL1: 3D structure…

PDB: 6SBV
Type: protein
Length: 2,630 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-lactate dehydrogenase a chain
EC: 1.1.1.27
UniProt: P00338
Ligands: L5K
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, F, H	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	329	45% helix, 21% strand	P00338
C, G	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	328	46% helix, 19% strand	P00338

Ligands and binding sites

L5K · ~{N}-[3-[(7-nitrodibenzofuran-2-yl) sulfonylamino]phenyl]-1-oxidanyl-cyclopropane-1-carboxamide · ligand · 8 copies · chains A, B, C, D, E, F, G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	857	0.85	0.87	103	empty
2	822	0.82	0.85	78	empty
3	606	0.80	0.86	55	empty
4	462	0.80	0.88	47	empty
5	414	0.76	0.86	54	empty

Interfaces

14 interfaces between chains.

A–B · 2651 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 2651 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 2648 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 2636 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 1302 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6SBV · X-ray Structure of Human LDH-A with an Allosteric Inhibitor (Compound 7) · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P00338
Elsewhere: RCSB PDB 6SBV · PDBe 6SBV · UniProt P00338

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