MolNFT v1 · #163243 · protein

Trypanosoma brucei PTR1 (TBPTR1) in complex with inhibitor 3 (nmt- C0013)

6RX0 · Pteridine reductase: “Trypanosoma brucei PTR1 (TBPTR1) in complex with inhibitor 3 (nmt- C0013)”. X-ray diffraction, 2 ligands (NAP, KM5), 7 pockets (best druggability 0.83). MolNFT v1 #163243 on GenesisL1: 3D structure, binding…

PDB: 6RX0
Type: protein
Length: 973 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pteridine reductase
UniProt: O76290
Ligands: NAP, KM5
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pteridine reductase	protein	248	48% helix, 15% strand	O76290
B, D	Pteridine reductase	protein	247	48% helix, 15% strand	O76290
C	Pteridine reductase	protein	231	48% helix, 16% strand	O76290

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
KM5 · methyl 1-[4-[[2,4-bis(azanyl)pteridin-6-yl]methyl-ethyl-amino]phenyl]carbonylpiperidine-4-carboxylate · ligand · 3 copies · chains A, B, D
ACT · Acetate ion · additive · chains A
GOL · Glycerol · additive · chains A

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	1162	0.83	0.84	70	empty
2	619	0.77	0.83	47	NAP, KM5
3	611	0.76	0.82	51	NAP, KM5
4	604	0.76	0.82	49	NAP, KM5
5	377	0.61	0.77	41	NAP

Interfaces

6 interfaces between chains.

B–D · 1829 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 1817 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1454 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1389 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 551 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6RX0 · Trypanosoma brucei PTR1 (TbPTR1) in complex with inhibitor 3 (NMT-C0013) · 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 6RX0 · PDBe 6RX0 · UniProt O76290

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