MolNFT v1 · #97586 · protein
Design and structural analysis of aromatic inhibitors of type II dehydroquinate dehydratase from mycobacterium tuberculosis - compound 49D [5-[(3-NITROBENZYL)OXY]BENZENE-1,3-dicarboxylic acid]
4KIU · 3-dehydroquinate dehydratase: “Design and structural analysis of aromatic inhibitors of type II dehydroquinate dehydratase from…”. X-ray diffraction, 1 ligand (KIU), 20 pockets (best druggability 0.79). MolNFT v1 #97586 on…
- PDB
- 4KIU
- Type
- protein
- Length
- 3,386 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
- KIU
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G, H, I, J, K, L, N, O, P, Q, R, S, T, U, V, W | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 141 | 42% helix, 18% strand | P0A4Z6 |
| D | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 143 | 46% helix, 18% strand | P0A4Z6 |
| M | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 135 | 47% helix, 19% strand | P0A4Z6 |
| X | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 147 | 44% helix, 18% strand | P0A4Z6 |
Ligands and binding sites
- KIU · 5-[(3-nitrobenzyl)oxy]benzene-1,3-dicarboxylic 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 | 1112 | 0.79 | 0.81 | 114 | empty |
| 2 | 150 | 0.77 | 0.94 | 27 | KIU |
| 3 | 103 | 0.77 | 0.97 | 20 | KIU |
| 4 | 145 | 0.76 | 0.94 | 26 | KIU |
| 5 | 91 | 0.76 | 0.98 | 22 | KIU |
Interfaces
41 interfaces between chains.
- D–I · 1020 Ų buried · 16 hydrogen bonds · protein-protein
- M–S · 1016 Ų buried · 16 hydrogen bonds · protein-protein
- C–H · 1010 Ų buried · 18 hydrogen bonds · protein-protein
- V–X · 1008 Ų buried · 19 hydrogen bonds · protein-protein
- P–U · 1000 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4KIU · 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 4KIU · PDBe 4KIU · UniProt P0A4Z6
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