MolNFT v1 · #151486 · protein
Structure of the kinase domain of human DDR1 in complex with a 2- amino-2,3-dihydro-1H-indene-5-carboxamide-based inhibitor
6HP9 · Epithelial discoidin domain-containing receptor 1: “Structure of the kinase domain of human DDR1 in complex with a 2…”. X-ray diffraction, 1 ligand (GKB), 4 pockets (best druggability 0.73). MolNFT v1 #151486 on GenesisL1: 3D…
- PDB
- 6HP9
- Type
- protein
- Length
- 578 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epithelial discoidin domain-containing receptor 1
- EC
- 2.7.10.1
- UniProt
- Q08345
- Ligands
- GKB
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 297 | 40% helix, 17% strand | Q08345 |
| B | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 281 | 43% helix, 17% strand | Q08345 |
Ligands and binding sites
- GKB · (2~{R})-~{N}-[3-(4-methylimidazol-1-yl)-5-(trifluoromethyl)phenyl]-2-(pyrimidin-5-ylamino)-2,3-dihydro-1~{H}-indene-5-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.73 | 0.78 | 67 | GKB |
| 2 | 621 | 0.71 | 0.79 | 55 | GKB |
| 3 | 388 | 0.62 | 0.78 | 39 | empty |
| 4 | 51 | 0.26 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 495 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6HP9 · Structure of the kinase domain of human DDR1 in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q08345 · AlphaFold monomer V2.0 prediction for epithelial discoidin domain- containing receptor 1… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q08345
- Elsewhere: RCSB PDB 6HP9 · PDBe 6HP9 · UniProt Q08345
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