MolNFT v1 · #149898 · protein

Trypanosoma brucei PTR1 in complex with inhibitor 4L (F162)

6GDP · Pteridine reductase: “Trypanosoma brucei PTR1 in complex with inhibitor 4L (F162)”. X-ray diffraction, 2 ligands (NAP, EVW), 8 pockets (best druggability 0.83). MolNFT v1 #149898 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6GDP
Type: protein
Length: 1,006 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pteridine reductase
UniProt: O76290
Ligands: NAP, EVW
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pteridine reductase	protein	252	46% helix, 15% strand	O76290
B	Pteridine reductase	protein	253	47% helix, 15% strand	O76290
C	Pteridine reductase	protein	251	47% helix, 15% strand	O76290
D	Pteridine reductase	protein	250	48% helix, 15% strand	O76290

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
EVW · 2-azanyl-~{N}-(diphenylmethyl)-1,3-benzothiazole-6-carboxamide · ligand · 3 copies · chains A, D, B, C
GOL · Glycerol · additive · 5 copies · chains A, B, D
ACT · Acetate ion · additive · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1122	0.83	0.84	70	empty
2	701	0.79	0.83	54	NAP, EVW
3	674	0.78	0.83	50	NAP, EVW
4	609	0.77	0.83	48	NAP
5	641	0.76	0.82	50	NAP, EVW, GOL

Interfaces

6 interfaces between chains.

B–D · 1899 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1894 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1422 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1399 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 562 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6GDP · Trypanosoma brucei PTR1 in complex with inhibitor 4l (F162) · 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 O76290
Elsewhere: RCSB PDB 6GDP · PDBe 6GDP · UniProt O76290

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