MolNFT v1 · #114368 · protein
Bianthranilate-like inhibitor with 6 atom "line" and phosphonate "hook" fishing for hydrogen bond donors in mycobacterium tuberculosis anthranilate phosphoribosyltransferase (anprt; trpd)
5BNE: “Bianthranilate-like inhibitor with 6 atom "line" and phosphonate "hook" fishing for hydrogen bond donors in…”. X-ray diffraction, 1 ligand (7P3), 15 pockets (best druggability 0.69). MolNFT v1 #114368 on GenesisL1: 3D structure…
- PDB
- 5BNE
- Type
- protein
- Length
- 1,326 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anthranilate phosphoribosyltransferase
- EC
- 2.4.2.18
- UniProt
- P9WFX5
- Ligands
- 7P3
- Pockets
- 15 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 335 | 55% helix, 12% strand | P9WFX5 |
| B | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 331 | 53% helix, 12% strand | P9WFX5 |
| C | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 333 | 54% helix, 12% strand | P9WFX5 |
| D | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 327 | 55% helix, 13% strand | P9WFX5 |
Ligands and binding sites
- 7P3 · 2-[(2-carboxyphenyl)amino]-5-[(5-phosphonopentyl)oxy]benzoic acid · ligand · 3 copies · chains A, B, D
- IMD · Imidazole · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.69 | 0.81 | 47 | 7P3 |
| 2 | 522 | 0.67 | 0.78 | 47 | 7P3 |
| 3 | 420 | 0.63 | 0.77 | 44 | empty |
| 4 | 296 | 0.62 | 0.80 | 46 | empty |
| 5 | 312 | 0.60 | 0.78 | 38 | 7P3 |
Interfaces
3 interfaces between chains.
- A–B · 860 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 850 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 534 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5BNE · Bianthranilate-like inhibitor with 6 atom line" and phosphonate "hook" fishing for… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WFX5 · AlphaFold monomer V2.0 prediction for anthranilate phosphoribosyltransferase (P9WFX5) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P9WFX5
- Elsewhere: RCSB PDB 5BNE · PDBe 5BNE · UniProt P9WFX5
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