Structure of PDB 5vd2 Chain A Binding Site BS01

Receptor Information
>5vd2 Chain A (length=258) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRYTTEFHELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQN
ALREVYAHAVLGQHSHVVRYFSAWAEDDHMLIQNEYCNGGSLADAISENY
RIMSYFKEAELKDLLLQVGRGLRYIHSMSLVHMDIKPSNIFISRKVMFKI
GDLGHVTRISSPQVEEGDSRFLANEVLQENYTHLPKADIFALALTVVCAA
GAEPLPRNGDQWHEIRQGRLPRIPQVLSQEFTELLKVMIHPDPERRPSAM
ALVKHSVL
Ligand information
Ligand ID34W
InChIInChI=1S/C23H25F3N6O2/c1-12(33)27-11-20(34)32-18-7-8-19(32)16-9-14(5-6-15(16)18)30-22-28-10-17(23(24,25)26)21(31-22)29-13-3-2-4-13/h5-6,9-10,13,18-19H,2-4,7-8,11H2,1H3,(H,27,33)(H2,28,29,30,31)/t18-,19+/m0/s1
InChIKeyRYYNGWLOYLRZLK-RBUKOAKNSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)NCC(=O)N1[CH]2CC[CH]1c3cc(Nc4ncc(c(NC5CCC5)n4)C(F)(F)F)ccc23
CACTVS 3.385CC(=O)NCC(=O)N1[C@H]2CC[C@@H]1c3cc(Nc4ncc(c(NC5CCC5)n4)C(F)(F)F)ccc23
ACDLabs 12.01FC(F)(F)c1c(nc(nc1)Nc2cc3c(cc2)C4N(C(=O)CNC(=O)C)C3CC4)NC5CCC5
OpenEye OEToolkits 1.7.6CC(=O)NCC(=O)N1C2CCC1c3c2ccc(c3)Nc4ncc(c(n4)NC5CCC5)C(F)(F)F
OpenEye OEToolkits 1.7.6CC(=O)NCC(=O)N1[C@H]2CC[C@@H]1c3c2ccc(c3)Nc4ncc(c(n4)NC5CCC5)C(F)(F)F
FormulaC23 H25 F3 N6 O2
NameN-{2-[(1S,4R)-6-{[4-(cyclobutylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-1,2,3,4-tetrahydro-1,4-epiminonaphthalen-9-yl]-2-oxoethyl}acetamide
ChEMBLCHEMBL4289017
DrugBankDB13059
ZINCZINC000043196229
PDB chain5vd2 Chain A Residue 601 [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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PDB5vd2 Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		E303 I305 F310 A326 E377 Y378 C379 G382 F433
Binding residue
(residue number reindexed from 1)		E11 I13 F18 A34 E85 Y86 C87 G90 F141
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.10,Kd=78.7nM
Enzymatic activity
Catalytic site (original residue number in PDB) D426 K428
Catalytic site (residue number reindexed from 1) D134 K136
Enzyme Commision number 2.7.10.2: non-specific protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

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Molecular Function
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Biological Process
External links
PDB RCSB:5vd2, PDBe:5vd2, PDBj:5vd2
PDBsum5vd2
PubMed28792760
UniProtP30291|WEE1_HUMAN Wee1-like protein kinase (Gene Name=WEE1)

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