MolNFT v1 · #179172 · protein
HER2 in complex with jbj-08-178-01
7JXH · Receptor tyrosine-protein kinase erbb-2: “HER2 in complex with jbj-08-178-01”. X-ray diffraction, 1 ligand (VOY), 20 pockets (best druggability 0.82). MolNFT v1 #179172 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7JXH
- Type
- protein
- Length
- 2,190 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-2
- EC
- 2.7.10.1
- UniProt
- P04626
- Ligands
- VOY
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 276 | 39% helix, 17% strand | P04626 |
| A | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 272 | 39% helix, 18% strand | P04626 |
| C | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 274 | 41% helix, 19% strand | P04626 |
| D | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 283 | 39% helix, 21% strand | P04626 |
| E | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 268 | 41% helix, 19% strand | P04626 |
| F | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 262 | 40% helix, 18% strand | P04626 |
| G | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 273 | 40% helix, 18% strand | P04626 |
| H | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 282 | 38% helix, 21% strand | P04626 |
Ligands and binding sites
- VOY · (2E)-N-[3-cyano-7-ethoxy-4-({3-methyl-4-[([1,2, 4]triazolo[1,5-a]pyridin-7-yl)oxy]phenyl}amino) quinolin-6-yl]-4-(dimethylamino)but-2-enamide · ligand · 8 copies · chains B, A, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.82 | 0.83 | 106 | VOY |
| 2 | 1133 | 0.81 | 0.82 | 84 | VOY |
| 3 | 1176 | 0.80 | 0.82 | 85 | VOY |
| 4 | 994 | 0.77 | 0.79 | 89 | VOY |
| 5 | 264 | 0.74 | 0.88 | 29 | VOY |
Interfaces
15 interfaces between chains.
- A–E · 1142 Ų buried · 9 hydrogen bonds · protein-protein
- D–G · 1077 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 773 Ų buried · 4 hydrogen bonds · protein-protein
- B–G · 615 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 560 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
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 P04626
- Elsewhere: RCSB PDB 7JXH · PDBe 7JXH · UniProt P04626
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