MolNFT v1 · #164866 · protein

Trypanosoma brucei PTR1 (TBPTR1) in complex with a tricyclic-based inhibitor

6TBX · Pteridine reductase: “Trypanosoma brucei PTR1 (TBPTR1) in complex with a tricyclic-based inhibitor”. X-ray diffraction, 2 ligands (NAP, N0Z), 7 pockets (best druggability 0.83). MolNFT v1 #164866 on GenesisL1: 3D structure, binding…

PDB: 6TBX
Type: protein
Length: 986 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pteridine reductase
UniProt: O76290
Ligands: NAP, N0Z
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, B	Pteridine reductase	protein	249	47% helix, 15% strand	O76290
C	Pteridine reductase	protein	239	49% helix, 15% strand	O76290
D	Pteridine reductase	protein	249	48% helix, 15% strand	O76290

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
N0Z · 2,4-bis(azanyl)-9~{H}-pyrimido[4,5-b]indol-6-ol · ligand · 4 copies · chains A, B, C, D
ACT · Acetate ion · additive · 2 copies · chains B, D
GOL · Glycerol · additive · chains C

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	67	empty
2	624	0.77	0.83	47	NAP, N0Z
3	591	0.75	0.82	46	NAP, N0Z
4	599	0.75	0.81	48	NAP, N0Z
5	451	0.66	0.78	43	NAP, N0Z

Interfaces

6 interfaces between chains.

B–C · 1876 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1833 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1404 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 1403 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 564 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

6TBX · Trypanosoma brucei PTR1 (TbPTR1) in complex with a tricyclic-based inhibitor · 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 6TBX · PDBe 6TBX · UniProt O76290

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