MolNFT v1 · #148712 · protein
Crystal structure of human DDR2 kinase in complex with 2-[4,5- difluoro-2-oxo-1'-(1H-PYRAZOLO[3,4-B]PYRIDINE-5-carbonyl) SPIRO[INDOLE-3,4'-piperidine]-1-yl]-N-(2,2,2-TRIFLUOROETHYL)ACETAMIDE
6FER · Discoidin domain-containing receptor 2: “Crystal structure of human DDR2 kinase in complex with 2-[4,5…”. X-ray diffraction, 1 ligand (D6Q), 20 pockets (best druggability 0.79). MolNFT v1 #148712 on GenesisL1: 3D structure, binding…
- PDB
- 6FER
- Type
- protein
- Length
- 3,275 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Discoidin domain-containing receptor 2
- EC
- 2.7.10.1
- UniProt
- Q16832
- Ligands
- D6Q
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 12 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Discoidin domain-containing receptor 2 (EC 2.7.10.1) | protein | 271 | 41% helix, 15% strand | Q16832 |
| B | Discoidin domain-containing receptor 2 (EC 2.7.10.1) | protein | 279 | 41% helix, 16% strand | Q16832 |
| C | Discoidin domain-containing receptor 2 (EC 2.7.10.1) | protein | 272 | 42% helix, 17% strand | Q16832 |
| D | Discoidin domain-containing receptor 2 (EC 2.7.10.1) | protein | 280 | 39% helix, 15% strand | Q16832 |
| E | Discoidin domain-containing receptor 2 (EC 2.7.10.1) | protein | 273 | 42% helix, 16% strand | Q16832 |
| F | Discoidin domain-containing receptor 2 (EC 2.7.10.1) | protein | 275 | 40% helix, 17% strand | Q16832 |
| G | Discoidin domain-containing receptor 2 (EC 2.7.10.1) | protein | 273 | 40% helix, 16% strand | Q16832 |
| H | Discoidin domain-containing receptor 2 (EC 2.7.10.1) | protein | 272 | 44% helix, 15% strand | Q16832 |
| I | Discoidin domain-containing receptor 2 (EC 2.7.10.1) | protein | 267 | 42% helix, 17% strand | Q16832 |
| J | Discoidin domain-containing receptor 2 (EC 2.7.10.1) | protein | 272 | 42% helix, 15% strand | Q16832 |
| K | Discoidin domain-containing receptor 2 (EC 2.7.10.1) | protein | 268 | 44% helix, 16% strand | Q16832 |
| L | Discoidin domain-containing receptor 2 (EC 2.7.10.1) | protein | 273 | 41% helix, 16% strand | Q16832 |
Ligands and binding sites
- D6Q · 2-[4,5-bis(fluoranyl)-2-oxidanylidene-1'-(1~{H}-pyrazolo[3,4-b]pyridin-5-ylcarbonyl)spiro[indole-3,4'-piperidine]-1-yl]-~{N}-[2,2,2-tris(fluoranyl) ethyl]ethanamide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 954 | 0.79 | 0.81 | 90 | D6Q |
| 2 | 920 | 0.76 | 0.79 | 80 | D6Q |
| 3 | 622 | 0.76 | 0.82 | 54 | D6Q |
| 4 | 1160 | 0.76 | 0.78 | 93 | D6Q |
| 5 | 1072 | 0.76 | 0.78 | 88 | D6Q |
Interfaces
22 interfaces between chains.
- B–L · 714 Ų buried · 3 hydrogen bonds · protein-protein
- A–H · 704 Ų buried · 5 hydrogen bonds · protein-protein
- H–K · 696 Ų buried · 3 hydrogen bonds · protein-protein
- D–I · 666 Ų buried · 5 hydrogen bonds · protein-protein
- A–K · 639 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6FER · Crystal Structure of human DDR2 kinase in complex with… · the same entry in another collection · chain L against L, 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 Q16832
- Elsewhere: RCSB PDB 6FER · PDBe 6FER · UniProt Q16832
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