MolNFT v1 · #114392 · protein
Bianthranilate-like inhibitor with 5 atom "line" and phosphonate "hook" fishing for hydrogen bond donors in mycobacterium tuberculosis anthranilate phosphoribosyltransferase (anprt; trpd)
5BO3: “Bianthranilate-like inhibitor with 5 atom "line" and phosphonate "hook" fishing for hydrogen bond donors in…”. X-ray diffraction, 1 ligand (7P2), 4 pockets (best druggability 0.65). MolNFT v1 #114392 on GenesisL1: 3D structure…
- PDB
- 5BO3
- Type
- protein
- Length
- 653 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anthranilate phosphoribosyltransferase
- EC
- 2.4.2.18
- UniProt
- A5U4M0
- Ligands
- 7P2
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 328 | 55% helix, 13% strand | A5U4M0 |
| B | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 325 | 55% helix, 13% strand | A5U4M0 |
Ligands and binding sites
- 7P2 · 2-[(2-carboxyphenyl)amino]-5-(4-phosphonobutoxy)benzoic acid · ligand · 2 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.65 | 0.79 | 50 | 7P2 |
| 2 | 407 | 0.65 | 0.79 | 37 | 7P2 |
| 3 | 94 | 0.37 | 0.75 | 19 | empty |
| 4 | 56 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 846 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5BO3 · Bianthranilate-like inhibitor with 5 atom line" and phosphonate "hook" fishing for… · the same entry in another collection · chain A against A, TM-score 1.00
- A5U4M0 · AlphaFold monomer V2.0 prediction for anthranilate phosphoribosyltransferase (A5U4M0) · a predicted model of the same protein · chain B 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 A5U4M0
- Elsewhere: RCSB PDB 5BO3 · PDBe 5BO3 · UniProt A5U4M0
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