MolNFT v1 · #68983 · protein
Crystal structure of tgfbri complexed with a pyrazolone inhibitor
3KCF · TGF-beta receptor type-1: “Crystal structure of tgfbri complexed with a pyrazolone inhibitor”. X-ray diffraction, 2 ligands (JZO, PO4), 20 pockets (best druggability 0.74). MolNFT v1 #68983 on GenesisL1: 3D structure, binding sites…
- PDB
- 3KCF
- Type
- protein
- Length
- 1,642 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TGF-beta receptor type-1
- EC
- 2.7.11.30
- UniProt
- P36897
- Ligands
- JZO, PO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TGF-beta receptor type-1 (EC 2.7.11.30) | protein | 328 | 39% helix, 15% strand | P36897 |
| B | TGF-beta receptor type-1 (EC 2.7.11.30) | protein | 324 | 41% helix, 17% strand | P36897 |
| C, D, E | TGF-beta receptor type-1 (EC 2.7.11.30) | protein | 330 | 39% helix, 15% strand | P36897 |
Ligands and binding sites
- JZO · 4-[3-(methoxymethyl)phenyl]-1,2-dimethyl-5-quinoxalin-6-yl-1,2-dihydro-3H-pyrazol-3-one · ligand · 5 copies · chains A, B, C, D, E
- PO4 · Phosphate ion · ion · 13 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.74 | 0.86 | 42 | JZO |
| 2 | 305 | 0.73 | 0.86 | 37 | JZO |
| 3 | 321 | 0.73 | 0.85 | 40 | JZO |
| 4 | 314 | 0.72 | 0.85 | 36 | JZO |
| 5 | 82 | 0.72 | 0.96 | 21 | empty |
Interfaces
5 interfaces between chains.
- D–E · 654 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 611 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 589 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 585 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 573 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3KCF · Crystal structure of TGFbRI complexed with a pyrazolone inhibitor · the same entry in another collection · chain E against E, TM-score 1.00
- P36897 · AlphaFold monomer V2.0 prediction for TGF-beta receptor type-1 (P36897) · 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 P36897
- Elsewhere: RCSB PDB 3KCF · PDBe 3KCF · UniProt P36897
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