Structure of PDB 5var Chain A Binding Site BS01

Receptor Information
>5var Chain A (length=108) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDI
VSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQL
VVKRDDVY
Ligand information
Ligand ID92Y
InChIInChI=1S/C16H23NO/c1-17(2)11-14-12-8-9-16(10-12,15(14)18)13-6-4-3-5-7-13/h3-7,12,14-15,18H,8-11H2,1-2H3/t12-,14-,15-,16+/m0/s1
InChIKeyHGNFUCJMHJYHIN-QCEMKRCNSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1cccc(c1)C32C(O)C(C(CC2)C3)CN(C)C
OpenEye OEToolkits 2.0.6CN(C)CC1C2CCC(C2)(C1O)c3ccccc3
CACTVS 3.385
OpenEye OEToolkits 2.0.6		CN(C)C[C@H]1[C@H]2CC[C@](C2)([C@H]1O)c3ccccc3
CACTVS 3.385CN(C)C[CH]1[CH]2CC[C](C2)([CH]1O)c3ccccc3
FormulaC16 H23 N O
Name(1R,2S,3R,4S)-3-[(dimethylamino)methyl]-1-phenylbicyclo[2.2.1]heptan-2-ol
ChEMBLCHEMBL5181544
DrugBank
ZINC
PDB chain5var Chain A Residue 1101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5var Targeting lysine specific demethylase 4A (KDM4A) tandem TUDOR domain - A fragment based approach.
Resolution1.83 Å
Binding residue
(original residue number in PDB)		F932 D934 S936 W967 Y973
Binding residue
(residue number reindexed from 1)		F36 D38 S40 W71 Y77
Annotation score1
Binding affinityMOAD: Kd=81.7uM
PDBbind-CN: -logKd/Ki=4.09,Kd=81.7uM
BindingDB: Kd=80000nM
Enzymatic activity
Enzyme Commision number 1.14.11.66: [histone H3]-trimethyl-L-lysine(9) demethylase.
1.14.11.69: [histone H3]-trimethyl-L-lysine(36) demethylase.
External links
PDB RCSB:5var, PDBe:5var, PDBj:5var
PDBsum5var
PubMed29691138
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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