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Crystal structure of a 6-cyclohexylmethyl-3-hydroxypyrimidine-2,4- dione inhibitor in complex with HIV reverse transcriptase
Analyse Crystal structure of a 6-cyclohexylmethyl-3-hydroxypyrimidine-2,4- dione… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TUQ
- Type
- protein
- Length
- 960 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase
- EC
- 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P03366
- Ligands
- J63, MG
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 555 | 31% helix, 22% strand | P03366 |
| B | HIV-1 reverse transcriptase (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 405 | 34% helix, 20% strand | P03366 |
Ligands and binding sites
- J63 · 1-[(benzyloxy)methyl]-6-(cyclohexylmethyl)-3-hydroxy-5-(propan-2-yl)pyrimidine-2,4(1H,3H)-dione · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.78 | 0.83 | 64 | empty |
| 2 | 717 | 0.76 | 0.81 | 74 | J63 |
| 3 | 228 | 0.67 | 0.84 | 40 | empty |
| 4 | 528 | 0.66 | 0.77 | 44 | empty |
| 5 | 188 | 0.65 | 0.85 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2701 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5TUQ · Crystal Structure of a 6-Cyclohexylmethyl-3-hydroxypyrimidine-2,4-dione Inhibitor in… · 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 5TUQ · PDBe 5TUQ · UniProt P03366
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