MolNFT v1 · #149897 · protein

Trypanosoma brucei PTR1 in complex with inhibitor 2G (F240)

6GDO · Pteridine reductase: “Trypanosoma brucei PTR1 in complex with inhibitor 2G (F240)”. X-ray diffraction, 2 ligands (NAP, EVZ), 7 pockets (best druggability 0.83). MolNFT v1 #149897 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6GDO
Type: protein
Length: 993 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pteridine reductase
UniProt: O76290
Ligands: NAP, EVZ
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Pteridine reductase	protein	248	48% helix, 15% strand	O76290
B	Pteridine reductase	protein	249	47% helix, 15% strand	O76290

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
EVZ · Methyl 1-[4-[(2-azanyl-1,3-benzothiazol-6-yl) sulfanylmethyl]phenyl]carbonylpiperidine-4-carboxylate · ligand · 3 copies · chains A, B, D
ACT · Acetate ion · additive · 2 copies · chains A, B
GOL · Glycerol · additive · chains B

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

Pockets

7 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	1160	0.83	0.84	68	empty
2	614	0.77	0.83	47	NAP, EVZ
3	626	0.76	0.82	50	NAP, EVZ
4	607	0.76	0.82	47	NAP
5	572	0.76	0.83	47	NAP, EVZ

Interfaces

6 interfaces between chains.

B–D · 1870 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 1851 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1443 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1412 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 553 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6GDO · Trypanosoma brucei PTR1 in complex with inhibitor 2g (F240) · 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 6GDO · PDBe 6GDO · UniProt O76290

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