MolNFT v1 · #114917 · protein

Crystal structure of HIV-1 reverse transcriptase (K101P) variant in complex with 8-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl) ETHOXY)PHENOXY)INDOLIZINE-2-carbonitrile (JLJ555), a non-nucleoside inhibitor

5C42 · HIV-1 reverse transcriptase, P66 subunit: “Crystal structure of HIV-1 reverse transcriptase (K101P) variant in complex with…”. X-ray diffraction, 1 ligand (29T), 19 pockets (best druggability 0.76). MolNFT v1 #114917 on GenesisL1…

PDB: 5C42
Type: protein
Length: 968 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 reverse transcriptase, P66 subunit; HIV-1 reverse transcriptase, P51 subunit
EC: 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
UniProt: P03366
Ligands: 29T
Pockets: 19 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HIV-1 reverse transcriptase, P66 subunit (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2)	protein	544	30% helix, 23% strand	P03366
B	HIV-1 reverse transcriptase, P51 subunit (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2)	protein	424	32% helix, 17% strand	P03366

Ligands and binding sites

29T · 8-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}indolizine-2-carbonitrile · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	287	0.76	0.88	40	29T
2	758	0.74	0.79	63	empty
3	813	0.73	0.78	63	empty
4	315	0.69	0.83	37	empty
5	287	0.65	0.82	32	empty

Interfaces

1 interface between chains.

A–B · 2534 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

5C42 · Crystal Structure of HIV-1 Reverse Transcriptase (K101P) Variant 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 P03366
Elsewhere: RCSB PDB 5C42 · PDBe 5C42 · UniProt P03366

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