PDB Entry (5ive)

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Visualizer: MichelaNGLo

PDB ID: 5ive Resolution: 1.78 Å Exp. Method: X-RAY DIFFRACTION
PMID: 27427228 DOI: 10.1016/j.chembiol.2016.06.006
Protein
Protein Name: Lysine-specific demethylase 5A
Protein Class: TRANSCRIPTION REGULATOR
Uniprot ID/ACC: P29375 (KDM5A_HUMAN) Organism: Homo sapiens
Gene Symbol: KDM5A Gene ID: 5927
Pocket Descriptors
Volume: 2086.02 Depth: 39.1714
Hydrophobicity: 0.677108 Drug Score: 0.999628
Pocket Similarity: Calculate
Ligand
Ligand Name:   5-methyl-7-oxo-6-(propan-2-yl)-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile
HET ID:   6E8 PubChem:   82273434
DrugBank:   - ChEMBL:   -
Canonical SMILES:   N#Cc1cnn2c1[nH]c(C)c(c2=O)C(C)C
Standard InChI:   InChI=1S/C11H12N4O/c1-6(2)9-7(3)14-10-8(4-12)5-13-15(10)11(9)16/h5-6,14H,1-3H3
Molecular Formula:   C11H12N4O Mol. Weight:   216.23918 Heavy Atoms:   16
Charge:   0 Is Chiral:   False logP:   1.32608
HBD:   1 HBA:   4 TPSA:   73.95
#Bonds:   18 #Rotatable Bonds:   1 Shape Complexity:   0.4
Stereocomplexity:   0.0 Ligand Type:   Small Molecule
Binding Affinity
Database Name Value
BindingDB Kd : 27 nM, Kd : 20 nM, Kd : 1500 nM, Kd : 490 nM
Binding MOAD Kd : 27 nM