Research workbench
Structural insights into mycobacterium tuberculosis CLPP1P2 inhibition by cediranib: implications for developing antimicrobial agents targeting clp protease
Analyse Structural insights into mycobacterium tuberculosis CLPP1P2 inhibition by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IW7
- Type
- protein
- Length
- 2,621 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit 2; ATP-dependent clp protease proteolytic…
- EC
- 3.4.21.92
- UniProt
- P9WPC2, P9WPC4
- Ligands
- BEZ, AV3
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 8 distinct chains · 46% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease proteolytic subunit 2 (EC 3.4.21.92) | protein | 194 | 43% helix, 26% strand | P9WPC2 |
| B | ATP-dependent clp protease proteolytic subunit 1 (EC 3.4.21.92) | protein | 177 | 50% helix, 23% strand | P9WPC4 |
| C, F, H | ATP-dependent clp protease proteolytic subunit 2 (EC 3.4.21.92) | protein | 196 | 43% helix, 28% strand | P9WPC2 |
| D, I, K | ATP-dependent clp protease proteolytic subunit 1 (EC 3.4.21.92) | protein | 175 | 49% helix, 25% strand | P9WPC4 |
| J | ATP-dependent clp protease proteolytic subunit 2 (EC 3.4.21.92) | protein | 195 | 43% helix, 28% strand | P9WPC2 |
| L, E | ATP-dependent clp protease proteolytic subunit 2 (EC 3.4.21.92) | protein | 193 | 44% helix, 28% strand | P9WPC2 |
| M, N, G | ATP-dependent clp protease proteolytic subunit 1 (EC 3.4.21.92) | protein | 176 | 49% helix, 24% strand | P9WPC4 |
| O, P, Q, R, T, U, V, W, X, Z, a, b, d, e | Bez-leu-leu | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 14 copies · chains J, K, O, P, A, B, Q, R, F, M, T, U, C, D, V, W, H, I, X, Z, E, G, a, b, L, N, d, e
- AV3 · 4-[(4-fluoro-2-methyl-3H-indol-5-yl)oxy]-6-methoxy-7-[3-(pyrrolidin-1-yl)propoxy]quinazoline · ligand · 7 copies · chains B, K, O, M, D, I, N, d, G, a, 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 | 942 | 0.74 | 0.77 | 87 | BEZ, AV3 |
| 2 | 889 | 0.73 | 0.77 | 88 | BEZ, AV3 |
| 3 | 935 | 0.73 | 0.77 | 88 | BEZ, AV3 |
| 4 | 935 | 0.73 | 0.77 | 89 | BEZ, AV3 |
| 5 | 903 | 0.72 | 0.77 | 87 | BEZ, AV3 |
Interfaces
62 interfaces between chains.
- H–E · 1778 Ų buried · 19 hydrogen bonds · protein-protein
- A–J · 1767 Ų buried · 22 hydrogen bonds · protein-protein
- C–H · 1766 Ų buried · 22 hydrogen bonds · protein-protein
- C–F · 1748 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 1686 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 covalent (covalent ligand).
Compared structures
- 6IW7 · structural insights into Mycobacterium tuberculosis ClpP1P2 inhibition by Cediranib… · the same entry in another collection · chain G against G, 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 P9WPC2
- Every structure of UniProt P9WPC4
- Elsewhere: RCSB PDB 6IW7 · PDBe 6IW7 · UniProt P9WPC2 · UniProt P9WPC4
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