Structure of PDB 3rwp Chain A Binding Site BS01

Receptor Information
>3rwp Chain A (length=278) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKEN
KVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIR
KIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQIT
DFGTAKVLSSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPP
FRAGNEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEME
GYGPLKAHPFFESVTWENLHQQTPPKLT
Ligand information
Ligand IDABQ
InChIInChI=1S/C24H24FN7O2/c1-13(2)32-9-16(21-23(26)28-12-29-24(21)32)22(33)18-7-27-8-20(30-18)31-19-11-34-10-17(19)14-3-5-15(25)6-4-14/h3-9,12-13,17,19H,10-11H2,1-2H3,(H,30,31)(H2,26,28,29)/t17-,19-/m1/s1
InChIKeyYXZBQCQAYNRRFP-IEBWSBKVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CC(C)n1cc(c2c1ncnc2N)C(=O)c3cncc(n3)NC4COCC4c5ccc(cc5)F
ACDLabs 12.01Fc1ccc(cc1)C5COCC5Nc4nc(C(=O)c3c2c(ncnc2n(c3)C(C)C)N)cnc4
CACTVS 3.370CC(C)n1cc(C(=O)c2cncc(N[CH]3COC[CH]3c4ccc(F)cc4)n2)c5c(N)ncnc15
CACTVS 3.370CC(C)n1cc(C(=O)c2cncc(N[C@@H]3COC[C@@H]3c4ccc(F)cc4)n2)c5c(N)ncnc15
OpenEye OEToolkits 1.7.2CC(C)n1cc(c2c1ncnc2N)C(=O)c3cncc(n3)N[C@@H]4COC[C@@H]4c5ccc(cc5)F
FormulaC24 H24 F N7 O2
Name[4-amino-7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl](6-{[(3S,4R)-4-(4-fluorophenyl)tetrahydrofuran-3-yl]amino}pyrazin-2-yl)methanone
ChEMBLCHEMBL1938415
DrugBank
ZINCZINC000073223440
PDB chain3rwp Chain A Residue 360 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3rwp Discovery of Novel, Potent, and Selective Inhibitors of 3-Phosphoinositide-Dependent Kinase (PDK1).
Resolution1.92 Å
Binding residue
(original residue number in PDB)		L88 G89 E90 G91 T95 V96 A109 K111 A162 E166 E209 L212 T222 D223
Binding residue
(residue number reindexed from 1)		L16 G17 E18 G19 T23 V24 A37 K39 A90 E94 E137 L140 T150 D151
Annotation score1
Binding affinityMOAD: Ki=0.6nM
PDBbind-CN: -logKd/Ki=9.22,Ki=0.6nM
BindingDB: Ki=0.600000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D205 K207 E209 N210 D223 T245
Catalytic site (residue number reindexed from 1) D133 K135 E137 N138 D151 T164
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3rwp, PDBe:3rwp, PDBj:3rwp
PDBsum3rwp
PubMed22040023
UniProtO15530|PDPK1_HUMAN 3-phosphoinositide-dependent protein kinase 1 (Gene Name=PDPK1)

[Back to BioLiP]