Structure of PDB 4xx9 Chain A

Receptor sequence

>4xx9A (length=289) Species: 9606 (Homo sapiens)

PPQPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIK
ENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKY
IRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQ
ITDFGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGC
IIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLD
ATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT

3D structure

• PDB: 4xx9 Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking.
• Chain: A
• Resolution: 1.4 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D205 K207 E209 N210 D223 T245
• Catalytic site (residue number reindexed from 1): D135 K137 E139 N140 D153 T175
• Enzyme Commision number: 2.7.11.1: non-specific serine/threonine protein kinase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ATP	A	G89 G91 S92 S94 V96 A109 K111 S160 A162 E166 L212	G19 G21 S22 S24 V26 A39 K41 S90 A92 E96 L142
BS02	RF4	A	K76 K115 I118 V127 R131 T148 L155 F157	K6 K45 I48 V57 R61 T78 L85 F87	PDBbind-CN: -logKd/Ki=5.08,Kd=8.4uM BindingDB: Kd=8000nM,EC50=2000nM
BS03	RF4	A	R172 G278 L279	R102 G208 L209	PDBbind-CN: -logKd/Ki=5.08,Kd=8.4uM BindingDB: Kd=8000nM,EC50=2000nM

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

External links

• PDB: RCSB:4xx9, PDBe:4xx9, PDBj:4xx9
• PDBsum: 4xx9
• PubMed: 26443011
• UniProt: O15530|PDPK1_HUMAN 3-phosphoinositide-dependent protein kinase 1 (Gene Name=PDPK1)