MolNFT v1 · #100943 · protein
Discovery of doravirine, an orally bioavailable non-nucleoside reverse transcriptase inhibitor potent against a wide range of resistant mutant HIV viruses
4NCG · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Discovery of doravirine, an orally bioavailable non-nucleoside reverse transcriptase inhibitor potent against…”. X-ray diffraction, 1 ligand (2KW), 12 pockets (best druggability 0.78). MolNFT…
- PDB
- 4NCG
- Type
- protein
- Length
- 955 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P04585
- Ligands
- 2KW
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 553 | 33% helix, 24% strand | P04585 |
| B | P51 rt (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 402 | 39% helix, 20% strand | P04585 |
Ligands and binding sites
- 2KW · 3-chloro-5-({1-[(4-methyl-5-oxo-4,5-dihydro-1H-1,2,4-triazol-3-yl)methyl]-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl}oxy)benzonitrile · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1196 | 0.78 | 0.80 | 130 | 2KW |
| 2 | 728 | 0.74 | 0.79 | 66 | empty |
| 3 | 246 | 0.68 | 0.84 | 40 | empty |
| 4 | 129 | 0.50 | 0.80 | 30 | empty |
| 5 | 204 | 0.47 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2957 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 4NCG · Discovery of Doravirine, an orally bioavailable non-nucleoside reverse transcriptase… · 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 P04585
- Elsewhere: RCSB PDB 4NCG · PDBe 4NCG · UniProt P04585
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