MolNFT v1 · #105044 · protein

Crystal structure of human muscle L-lactate dehydrogenase in complex with inhibitor 1, 3-{[3-carbamoyl-7-(2,4-dimethoxypyrimidin-5-yl) quinolin-4-YL]AMINO}BENZOIC acid

4QT0 · L-lactate dehydrogenase a chain: “Crystal structure of human muscle L-lactate dehydrogenase in complex with inhibitor 1…”. X-ray diffraction, 1 ligand (38Q), 20 pockets (best druggability 0.89). MolNFT v1 #105044 on GenesisL1: 3D…

PDB: 4QT0
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: 38Q
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 20% 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, 21% strand	P00338
B, E, F, G, H	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	331	44% helix, 18% strand	P00338

Ligands and binding sites

38Q · 3-{[3-carbamoyl-7-(2,4-dimethoxypyrimidin-5-yl)quinolin-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	1160	0.89	0.91	117	empty
2	1140	0.89	0.91	113	empty
3	68	0.69	0.96	16	empty
4	71	0.69	0.95	14	empty
5	66	0.68	0.95	14	empty

Interfaces

14 interfaces between chains.

C–D · 2834 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2818 Å² buried · 27 hydrogen bonds · protein-protein
G–H · 2798 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 2798 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 1828 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

4QT0 · Crystal structure of human muscle L-lactate dehydrogenase in complex with inhibitor 1… · 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 4QT0 · PDBe 4QT0 · UniProt P00338

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