Structure of PDB 6mdb Chain A Binding Site BS01

Receptor Information
>6mdb Chain A (length=487) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVT
HIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKGDVIELKYPLNCA
DPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQPGDFVLSVRTGDSK
VTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPL
NTTRINAAEIESRVRELSKLQGFWEEFETLQQQECKLLYSRKEGQRQENK
NKNRYKNILPFDHTRVVLHDGDPPVSDYINANIIMPKSYIATQGCLQNTV
NDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNV
KESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDF
LEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDI
DVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETL
Ligand information
Ligand IDJE4
InChIInChI=1S/C18H20Cl2N6O/c1-18(21)6-8-26(9-7-18)17-22-15-12(16(27)25(17)2)14(23-24-15)10-4-3-5-11(19)13(10)20/h3-5H,6-9,21H2,1-2H3,(H,23,24)
InChIKeyMSUDNEADKNPNRJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1C(=O)c2c([nH]nc2c3cccc(Cl)c3Cl)N=C1N4CCC(C)(N)CC4
OpenEye OEToolkits 2.0.6CC1(CCN(CC1)C2=Nc3c(c(n[nH]3)c4cccc(c4Cl)Cl)C(=O)N2C)N
ACDLabs 12.01c13c(nnc1c2c(c(Cl)ccc2)Cl)N=C(N(C3=O)C)N4CCC(C)(CC4)N
FormulaC18 H20 Cl2 N6 O
Name6-(4-amino-4-methylpiperidin-1-yl)-3-(2,3-dichlorophenyl)-5-methyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL4469071
DrugBank
ZINC
PDB chain6mdb 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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PDB6mdb 6-Amino-3-methylpyrimidinones as Potent, Selective, and Orally Efficacious SHP2 Inhibitors.
Resolution2.34 Å
Binding residue
(original residue number in PDB)		R111 F113 H114 T219 E249 E250 T253 L254 Q257 P491 K492 Q495
Binding residue
(residue number reindexed from 1)		R106 F108 H109 T203 E225 E226 T229 L230 Q233 P453 K454 Q457
Annotation score1
Binding affinityMOAD: ic50=0.064uM
PDBbind-CN: -logKd/Ki=7.17,IC50=0.067uM
Enzymatic activity
Catalytic site (original residue number in PDB) D425 C459 R465 T466 Q506
Catalytic site (residue number reindexed from 1) D387 C421 R427 T428 Q468
Enzyme Commision number 3.1.3.48: protein-tyrosine-phosphatase.
Gene Ontology
Molecular Function
GO:0004725 protein tyrosine phosphatase activity
Biological Process
GO:0006470 protein dephosphorylation
GO:0016311 dephosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6mdb, PDBe:6mdb, PDBj:6mdb
PDBsum6mdb
PubMed30688459
UniProtQ06124|PTN11_HUMAN Tyrosine-protein phosphatase non-receptor type 11 (Gene Name=PTPN11)

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