Research workbench
Mycobacterium tuberculosis RV2671 complexed with beta-NADPH and 6- ethyl-5-{(3S)-3-[2-methoxy-5-(pyridin-4-YL)PHENYL]BUT-1-yn-1- YL}PYRIMIDINE-2,4-diamine
Analyse Mycobacterium tuberculosis RV2671 complexed with beta-NADPH and 6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DE5
- Type
- protein
- Length
- 246 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboflavin biosynthesis protein ribd
- UniProt
- P71968
- Ligands
- NDP, G8J
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Riboflavin biosynthesis protein ribd | protein | 246 | 26% helix, 22% strand | P71968 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- G8J · 6-ethyl-5-{(3S)-3-[2-methoxy-5-(pyridin-4-yl) phenyl]but-1-yn-1-yl}pyrimidine-2,4-diamine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.64 | 0.79 | 34 | G8J |
| 2 | 184 | 0.48 | 0.75 | 28 | empty |
| 3 | 155 | 0.44 | 0.75 | 19 | empty |
| 4 | 93 | 0.37 | 0.75 | 19 | NDP |
Compared structures
- 6DE5 · Mycobacterium tuberculosis Rv2671 complexed with beta-NADPH and… · 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 P71968
- Elsewhere: RCSB PDB 6DE5 · PDBe 6DE5 · UniProt P71968
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