MolNFT v1 · #169422 · protein
Structure of ndm-1 in complex with macrocycle inhibitor NDM1I-1G
6XBF · Blandm-4_1_JQ348841: “Structure of ndm-1 in complex with macrocycle inhibitor NDM1I-1G”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.78). MolNFT v1 #169422 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6XBF
- Type
- protein
- Length
- 948 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blandm-4_1_JQ348841; Macrocycle inhibitor NDM1I-1G
- UniProt
- E9NWK5
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Blandm-4_1_JQ348841 | protein | 229 | 26% helix, 32% strand | E9NWK5 |
| F, G, H, I | Macrocycle inhibitor NDM1I-1G | protein | 8 | 0% helix, 25% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, F, B, G, C, H, D, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.78 | 0.97 | 21 | empty |
| 2 | 1168 | 0.72 | 0.75 | 82 | empty |
| 3 | 85 | 0.53 | 0.85 | 28 | empty |
| 4 | 105 | 0.45 | 0.79 | 29 | empty |
| 5 | 88 | 0.44 | 0.80 | 20 | empty |
Interfaces
8 interfaces between chains.
- B–C · 924 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 477 Ų buried · 1 hydrogen bond · protein-protein
- B–G · 444 Ų buried · 1 hydrogen bond · protein-protein
- D–I · 420 Ų buried · 6 hydrogen bonds · protein-protein
- C–H · 414 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 d-amino (D-amino acid).
Compared structures
- 6XBF · Structure of NDM-1 in complex with macrocycle inhibitor NDM1i-1G · 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 E9NWK5
- Elsewhere: RCSB PDB 6XBF · PDBe 6XBF · UniProt E9NWK5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.