GL1X · GenesisL1 explorer

MolNFT v1 · #142221 · protein

Crystal structure of ACK1 with compound 10D

5ZXB · Activated CDC42 kinase 1: “Crystal structure of ACK1 with compound 10D”. X-ray diffraction, 1 ligand (9KO), 3 pockets (best druggability 0.69). MolNFT v1 #142221 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
5ZXB
Type
protein
Length
481 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Activated CDC42 kinase 1
EC
2.7.10.2, 2.7.11.1
UniProt
Q07912
Ligands
9KO
Pockets
3 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AActivated CDC42 kinase 1 (EC 2.7.10.2, 2.7.11.1)protein24045% helix, 20% strandQ07912
BActivated CDC42 kinase 1 (EC 2.7.10.2, 2.7.11.1)protein24143% helix, 20% strandQ07912

Ligands and binding sites

  • 9KO · N-{3-[7-{[6-(4-acetylpiperazin-1-yl)pyridin-3-yl]amino}-1-methyl-2-oxo-1,4-dihydropyrimido[4,5-d]pyrimidin-3(2H)-yl]-4-methylphenyl}-3-(trifluoromethyl)benzamide · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13430.690.82369KO
23180.680.82359KO
32500.500.7547empty

Interfaces

1 interface between chains.

  • A–B · 622 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

  • 5ZXB · Crystal structure of ACK1 with compound 10d · the same entry in another collection · chain A against A, TM-score 1.00
  • Q07912 · AlphaFold monomer V2.0 prediction for activated CDC42 kinase 1 (Q07912) · a predicted model of the same protein · chain B against A, TM-score 0.95

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