MolNFT v1 · #95219 · protein
Crystal structure of human PRPF4B kinase domain in complex with 4-{5- [(2-chloro-pyridin-4-ylmethyl)-carbamoyl]-thiophen-2-yl}- BENZO[B]THIOPHENE-2-carboxylic acid amine
4IJP · SERINE/THREONINE-protein kinase PRP4 homolog: “Crystal structure of human PRPF4B kinase domain in complex with 4-{5…”. X-ray diffraction, 2 ligands (1EH, SO4), 6 pockets (best druggability 0.69). MolNFT v1 #95219 on GenesisL1: 3D…
- PDB
- 4IJP
- Type
- protein
- Length
- 665 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PRP4 homolog
- EC
- 2.7.11.1
- UniProt
- Q13523
- Ligands
- 1EH, SO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PRP4 homolog (EC 2.7.11.1) | protein | 331 | 39% helix, 18% strand | Q13523 |
| B | SERINE/THREONINE-protein kinase PRP4 homolog (EC 2.7.11.1) | protein | 334 | 40% helix, 18% strand | Q13523 |
Ligands and binding sites
- 1EH · 4-(5-{[(2-chloropyridin-4-yl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.69 | 0.85 | 34 | 1EH |
| 2 | 448 | 0.68 | 0.80 | 54 | 1EH |
| 3 | 68 | 0.56 | 0.88 | 20 | SO4 |
| 4 | 93 | 0.33 | 0.73 | 13 | empty |
| 5 | 76 | 0.32 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 634 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4IJP · Crystal Structure of Human PRPF4B kinase domain in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13523 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase PRP4 homolog… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q13523
- Elsewhere: RCSB PDB 4IJP · PDBe 4IJP · UniProt Q13523
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