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Crystal structure of human muscle L-lactate dehydrogenase in complex with inhibitor 2, 3-{[7-(2,4-dimethoxypyrimidin-5-yl)-3- sulfamoylquinolin-4-YL]AMINO}BENZOIC acid

Analyse Crystal structure of human muscle L-lactate dehydrogenase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QSM
Type: protein
Length: 2,651 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: 38K
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	332	44% helix, 19% strand	P00338
B, E, F, G, H	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	331	45% helix, 19% strand	P00338

Ligands and binding sites

38K · 3-{[7-(2,4-dimethoxypyrimidin-5-yl)-3-sulfamoylquinolin-4-yl]amino}benzoic acid · ligand · 8 copies · chains A, B, H, C, D, E, F, G

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1179	0.90	0.91	119	empty
2	1088	0.89	0.91	115	empty
3	57	0.68	0.96	16	empty
4	575	0.66	0.77	55	38K
5	53	0.66	0.96	15	empty

Interfaces

14 interfaces between chains.

C–D · 2880 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 2861 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2854 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 2820 Å² buried · 25 hydrogen bonds · protein-protein
F–G · 1822 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

4QSM · Crystal structure of human muscle L-lactate dehydrogenase in complex with inhibitor 2… · the same entry in another collection · chain E against E, 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 4QSM · PDBe 4QSM · UniProt P00338

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