Research workbench
Design and structural analysis of aromatic inhibitors of type II dehydroquinate dehydratase from mycobacterium tuberculosis - compound 49E [5-[(3-NITROBENZYL)AMINO]BENZENE-1,3-dicarboxylic acid]
Analyse Design and structural analysis of aromatic inhibitors of type II dehydroquinate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KIW
- Type
- protein
- Length
- 3,348 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
- KIW
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G, H, I, J, K, M, N, O, P, S, U, W | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 141 | 44% helix, 18% strand | P0A4Z6 |
| C, L, R, X | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 138 | 46% helix, 18% strand | P0A4Z6 |
| D, V | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 137 | 42% helix, 18% strand | P0A4Z6 |
| E, F, Q | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 136 | 46% helix, 18% strand | P0A4Z6 |
| T | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 140 | 41% helix, 18% strand | P0A4Z6 |
Ligands and binding sites
- KIW · 5-[(3-nitrobenzyl)amino]benzene-1,3-dicarboxylic acid · ligand · 22 copies · chains A, L, B, E, C, D, G, F, H, J, I, K, M, X, N, Q, O, P, S, R, T, V, U, W
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 | 214 | 0.78 | 0.93 | 31 | KIW |
| 2 | 158 | 0.74 | 0.92 | 24 | KIW |
| 3 | 376 | 0.74 | 0.85 | 35 | KIW |
| 4 | 150 | 0.74 | 0.92 | 28 | empty |
| 5 | 141 | 0.74 | 0.93 | 29 | KIW |
Interfaces
40 interfaces between chains.
- N–R · 1033 Ų buried · 17 hydrogen bonds · protein-protein
- M–S · 1023 Ų buried · 16 hydrogen bonds · protein-protein
- J–L · 1019 Ų buried · 21 hydrogen bonds · protein-protein
- C–H · 1010 Ų buried · 18 hydrogen bonds · protein-protein
- D–I · 1010 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4KIW · Design and structural analysis of aromatic inhibitors of type II dehydroquinate… · 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 P0A4Z6
- Elsewhere: RCSB PDB 4KIW · PDBe 4KIW · UniProt P0A4Z6
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