Research workbench
Encoded library technology as a source of hits for the discovery and lead optimization of a potent and selective class of bactericidal direct inhibitors of mycobacterium tuberculosis inha
Analyse Encoded library technology as a source of hits for the discovery and lead… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4COD
- Type
- protein
- Length
- 1,072 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enoyl-[acyl-carrier-protein] reductase [NADH]
- EC
- 1.3.1.9
- UniProt
- P0A5Y6
- Ligands
- KV1, NAD
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, F, H | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 268 | 45% helix, 17% strand | P0A5Y6 |
Ligands and binding sites
- KV1 · N-((3R,5S)-1-(benzofuran-3-carbonyl)-5-(ethylcarbamoyl)pyrrolidin-3-yl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamide · ligand · 4 copies · chains B, D, F, H
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.83 | 0.85 | 54 | empty |
| 2 | 622 | 0.80 | 0.85 | 51 | KV1, NAD |
| 3 | 552 | 0.79 | 0.85 | 50 | KV1, NAD |
| 4 | 568 | 0.79 | 0.85 | 51 | NAD, KV1 |
| 5 | 582 | 0.79 | 0.85 | 51 | KV1, NAD |
Interfaces
6 interfaces between chains.
- D–H · 1595 Ų buried · 19 hydrogen bonds · protein-protein
- B–F · 1575 Ų buried · 17 hydrogen bonds · protein-protein
- B–H · 1531 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1529 Ų buried · 19 hydrogen bonds · protein-protein
- F–H · 719 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4COD · Encoded library technology as a source of hits for the discovery and lead optimization of… · the same entry in another collection · chain B against B, 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 P0A5Y6
- Elsewhere: RCSB PDB 4COD · PDBe 4COD · UniProt P0A5Y6
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