3QD4	Transferase Transferase Inhibitor	date	Jan 17, 2011
title	Phosphoinositide-Dependent Kinase-1 (Pdk1) Kinase Domain Wit Dimethylethyl{(3r,5r)-1-[2-Amino-6-(3-Amino-1h-Indazol-6-Yl Pyrimidinyl]-5-Methyl-3-Piperidinyl}Carbamate
authors	J.R.Medina, C.J.Becker, C.W.Blackledge, C.Duquenne, Y.Feng, S.W.G D.Heerding, W.H.Li, W.H.Miller, S.P.Romeril, D.Scherzer, A.Shu, M A.R.Chadderton, M.Dumble, C.M.Gradiner, S.Gilbert, Q.Liu, S.K.Ra V.Sudakin, H.Xiang, P.G.Brady, N.Campobasso, P.Ward, J.M.Axten
compound		source
Molecule: 3-Phosphoinositide-Dependent Protein Kinase 1 Chain: A Fragment: Kinase Domain, Residues 48-359 Synonym: Hpdk1 Ec: 2.7.11.1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Pdk1, Pdpk1 Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108
symmetry	Space Group: P 32 2 1	R_factor 0.194 R_Free 0.244
crystal cell	length a length b length c angle alpha angle beta angle gamma 124.315 124.315 47.017 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	3Q6, SO4 BindingDB	enzyme	Transferase E.C.2.7.11.1 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Structure-Based Design of Potent and Selective 3-Phosphoinositide-Dependent Kinase-1 (PDK1) Inhibitors., Medina JR, Becker CJ, Blackledge CW, Duquenne C, Feng Y, Grant SW, Heerding D, Li WH, Miller WH, Romeril SP, Scherzer D, Shu A, Bobko MA, Chadderton AR, Dumble M, Gardiner CM, Gilbert S, Liu Q, Rabindran SK, Sudakin V, Xiang H, Brady PG, Campobasso N, Ward P, Axten JM, J Med Chem. 2011 Feb 22. PMID:21341675

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk] Biological Unit Coordinates (3qd4.pdb1.gz) 47 Kb LPC: Ligand-Protein Contacts for 3QD4 CSU: Contacts of Structural Units for 3QD4 Structure Factors (230 Kb) Retrieve 3QD4 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3QD4 from S2C, [Save to disk] Re-refined 3qd4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3QD4 in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 3QD4

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3QD4, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3qd4] [3qd4_A] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3QD4: [S_TKc ] by SMART

Other resources with information on 3QD4

Community annotation for 3QD4 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---