MolNFT v1 · #169214 · protein
Crystal structure of HIV-1 reverse transcriptase in complex with methyl 2-(6-cyano-3-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl) ETHOXY)PHENOXY)-4-methylnaphthalen-1-YL)ACETATE (JLJ681), a non- nucleoside inhibitor
6X4E · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Crystal structure of HIV-1 reverse transcriptase in complex with methyl…”. X-ray diffraction, 2 ligands (UMV, SO4), 14 pockets (best druggability 0.80). MolNFT v1 #169214 on GenesisL1: 3D…
- PDB
- 6X4E
- Type
- protein
- Length
- 948 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
- UniProt
- P03366
- Ligands
- UMV, SO4
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% 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) | protein | 547 | 30% helix, 24% strand | P03366 |
| B | P51 rt | protein | 401 | 37% helix, 20% strand | P03366 |
Ligands and binding sites
- UMV · methyl (6-cyano-3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-4-methylnaphthalen-1-yl)acetate · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.80 | 0.86 | 68 | UMV |
| 2 | 744 | 0.78 | 0.82 | 63 | empty |
| 3 | 494 | 0.69 | 0.80 | 55 | empty |
| 4 | 616 | 0.67 | 0.76 | 46 | empty |
| 5 | 256 | 0.62 | 0.80 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2731 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6X4E · Crystal Structure of HIV-1 Reverse Transcriptase in Complex with methyl… · 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 P03366
- Elsewhere: RCSB PDB 6X4E · PDBe 6X4E · UniProt P03366
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