Research workbench
Design and structural analysis of aromatic inhibitors of type II dehydroquinase from mycobacterium tuberculosis - compound 41C [3- hydroxy-5-(3-NITROPHENOXY)BENZOIC acid]
Analyse Design and structural analysis of aromatic inhibitors of type II dehydroquinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KI7
- Type
- protein
- Length
- 3,379 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- P0A4Z6
- Ligands
- 1R2
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 134 | 48% helix, 17% strand | P0A4Z6 |
| B, C, E, F, G, H, I, J, K, L, N, O, P, R, T, U, V, W | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 141 | 47% helix, 18% strand | P0A4Z6 |
| D | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 143 | 46% helix, 17% strand | P0A4Z6 |
| M | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 137 | 46% helix, 18% strand | P0A4Z6 |
| Q | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 137 | 45% helix, 18% strand | P0A4Z6 |
| S | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 140 | 44% helix, 14% strand | P0A4Z6 |
| X | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 150 | 43% helix, 17% strand | P0A4Z6 |
Ligands and binding sites
- 1R2 · 3-hydroxy-5-(3-nitrophenoxy)benzoic acid · ligand · 22 copies · chains A, L, B, E, C, D, G, F, H, J, I, K, N, Q, O, P, S, R, T, V, U, M, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.77 | 0.94 | 26 | 1R2 |
| 2 | 128 | 0.77 | 0.96 | 25 | 1R2 |
| 3 | 1116 | 0.76 | 0.78 | 93 | empty |
| 4 | 88 | 0.76 | 0.98 | 23 | 1R2 |
| 5 | 100 | 0.76 | 0.97 | 22 | 1R2 |
Interfaces
41 interfaces between chains.
- D–I · 1026 Ų buried · 16 hydrogen bonds · protein-protein
- M–S · 1016 Ų buried · 17 hydrogen bonds · protein-protein
- V–X · 1011 Ų buried · 17 hydrogen bonds · protein-protein
- C–H · 1003 Ų buried · 17 hydrogen bonds · protein-protein
- J–L · 1000 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4KI7 · Design and structural analysis of aromatic inhibitors of type II dehydroquinase from… · the same entry in another collection · chain B against B, 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 P0A4Z6
- Elsewhere: RCSB PDB 4KI7 · PDBe 4KI7 · UniProt P0A4Z6
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