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Co-crystal structure of human nicotinamiden-methyltransferase (nnmt) in complex with high-affinity alkynyl bisubstrate inhibitor NS1
Analyse Co-crystal structure of human nicotinamiden-methyltransferase (nnmt) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ORR
- Type
- protein
- Length
- 1,058 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nnmt protein
- UniProt
- Q6FH49
- Ligands
- N37
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nnmt protein | protein | 271 | 36% helix, 24% strand | Q6FH49 |
| B, D | Nnmt protein | protein | 257 | 38% helix, 25% strand | Q6FH49 |
| C | Nnmt protein | protein | 273 | 35% helix, 24% strand | Q6FH49 |
Ligands and binding sites
- N37 · 9-{9-amino-6-[(3-carbamoylphenyl)ethynyl]-5,6,7,8,9-pentadeoxy-D-glycero-alpha-L-talo-decofuranuronosyl}-9H-purin-6-amine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.81 | 0.94 | 43 | N37 |
| 2 | 219 | 0.80 | 0.93 | 41 | N37 |
| 3 | 216 | 0.80 | 0.93 | 44 | N37 |
| 4 | 568 | 0.77 | 0.84 | 84 | GOL, N37 |
| 5 | 568 | 0.69 | 0.78 | 77 | empty |
Interfaces
4 interfaces between chains.
- A–C · 618 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 472 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 446 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 435 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6ORR · Co-crystal structure of human NicotinamideN-Methyltransferase (NNMT) in complex with… · 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 Q6FH49
- Elsewhere: RCSB PDB 6ORR · PDBe 6ORR · UniProt Q6FH49
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