Structure of PDB 6di1 Chain A Binding Site BS01

Receptor Information
>6di1 Chain A (length=271) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMS
EDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLRE
MRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVS
DFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMW
EIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKA
DERPTFKILLSNILDVMDEES
Ligand information
Ligand IDGJD
InChIInChI=1S/C12H18N6O2/c1-2-9(19)16-7-3-4-18(6-7)12-15-5-8(11(14)20)10(13)17-12/h5,7H,2-4,6H2,1H3,(H2,14,20)(H,16,19)(H2,13,15,17)/t7-/m0/s1
InChIKeyRFNYKYSEMVFRHS-ZETCQYMHSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1(nc(N)c(C(=O)N)cn1)N2CC(NC(CC)=O)CC2
OpenEye OEToolkits 2.0.6CCC(=O)NC1CCN(C1)c2ncc(c(n2)N)C(=O)N
CACTVS 3.385CCC(=O)N[CH]1CCN(C1)c2ncc(C(N)=O)c(N)n2
OpenEye OEToolkits 2.0.6CCC(=O)N[C@H]1CCN(C1)c2ncc(c(n2)N)C(=O)N
CACTVS 3.385CCC(=O)N[C@H]1CCN(C1)c2ncc(C(N)=O)c(N)n2
FormulaC12 H18 N6 O2
Name4-amino-2-[(3S)-3-(propanoylamino)pyrrolidin-1-yl]pyrimidine-5-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6di1 Chain A Residue 701 [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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PDB6di1 Discovery of a novel series of pyridine and pyrimidine carboxamides as potent and selective covalent inhibitors of Btk.
Resolution1.1 Å
Binding residue
(original residue number in PDB)		L408 T410 G411 A428 Y476 M477 C481 L528
Binding residue
(residue number reindexed from 1)		L20 T22 G23 A40 Y88 M89 C93 L140
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.74,IC50=180nM
Enzymatic activity
Catalytic site (original residue number in PDB) D521 A523 R525 N526 D539
Catalytic site (residue number reindexed from 1) D133 A135 R137 N138 D151
Enzyme Commision number 2.7.10.2: non-specific protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:6di1, PDBe:6di1, PDBj:6di1
PDBsum6di1
PubMed30290988
UniProtQ06187|BTK_HUMAN Tyrosine-protein kinase BTK (Gene Name=BTK)

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