Structure of PDB 4nct Chain A Binding Site BS01

Receptor Information
>4nct Chain A (length=342) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQE
WVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNH
LCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSI
IHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVL
LGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAH
ILDQAPKARKFFEKLPDGTWNLKKTEYKPPGTRKLHNILGVETGGPGGRR
AGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFK
Ligand information
Ligand ID2K2
InChIInChI=1S/C35H30N4O4/c1-35-32(42-3)25(37(2)34(41)19-11-5-4-6-12-19)17-26(43-35)38-23-15-9-7-13-20(23)28-29-22(18-36-33(29)40)27-21-14-8-10-16-24(21)39(35)31(27)30(28)38/h4-16,25-26,32H,17-18H2,1-3H3,(H,36,40)/t25-,26-,32-,35+/m1/s1
InChIKeyBMGQWWVMWDBQGC-IIFHNQTCSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(c1ccccc1)N(C9C(OC)C8(OC(n6c5c3n8c2ccccc2c3c4c(C(=O)NC4)c5c7ccccc67)C9)C)C
OpenEye OEToolkits 1.7.6C[C@@]12[C@@H]([C@@H](C[C@@H](O1)n3c4ccccc4c5c3c6n2c7ccccc7c6c8c5C(=O)NC8)N(C)C(=O)c9ccccc9)OC
CACTVS 3.385CO[C@@H]1[C@@H](C[C@H]2O[C@]1(C)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35)N(C)C(=O)c9ccccc9
OpenEye OEToolkits 1.7.6CC12C(C(CC(O1)n3c4ccccc4c5c3c6n2c7ccccc7c6c8c5C(=O)NC8)N(C)C(=O)c9ccccc9)OC
CACTVS 3.385CO[CH]1[CH](C[CH]2O[C]1(C)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35)N(C)C(=O)c9ccccc9
FormulaC35 H30 N4 O4
NamePKC412;
N-[(5S,6R,7R,9R)-6-methoxy-5-methyl-14-oxo-6,7,8,9,15,16-hexahydro-5H,14H-5,9-epoxy-4b,9a,15-triazadibenzo[b,h]cyclonon a[1,2,3,4-jkl]cyclopenta[e]-as-indacen-7-yl]-N-methylbenzamide
ChEMBLCHEMBL608533
DrugBankDB06595
ZINCZINC000100013130
PDB chain4nct Chain A Residue 501 [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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PDB4nct The structure of a dual-specificity tyrosine phosphorylation-regulated kinase 1A-PKC412 complex reveals disulfide-bridge formation with the anomalous catalytic loop HRD(HCD) cysteine.
Resolution2.597 Å
Binding residue
(original residue number in PDB)		I165 G166 V173 A186 M240 E291 D307
Binding residue
(residue number reindexed from 1)		I32 G33 V40 A53 M107 E158 D174
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.55,Ki=28.4nM
BindingDB: Kd=100nM
Enzymatic activity
Catalytic site (original residue number in PDB) D287 K289 N292 D307 S324
Catalytic site (residue number reindexed from 1) D154 K156 N159 D174 S191
Enzyme Commision number 2.7.11.23: [RNA-polymerase]-subunit kinase.
2.7.12.1: dual-specificity kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004712 protein serine/threonine/tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation
GO:0046777 protein autophosphorylation

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Molecular Function
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Biological Process
External links
PDB RCSB:4nct, PDBe:4nct, PDBj:4nct
PDBsum4nct
PubMed25945585
UniProtQ13627|DYR1A_HUMAN Dual specificity tyrosine-phosphorylation-regulated kinase 1A (Gene Name=DYRK1A)

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