5KOT

Discovery of TAK-272: A Novel, Potent and Orally Active Renin In-hibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.203 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 6VUClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Discovery of TAK-272: A Novel, Potent and Orally Active Renin Inhibitor

Imaeda, Y.Tokuhara, H.Fukase, Y.Kanagawa, R.Kajimoto, Y.Kusumoto, K.Kondo, M.Snell, G.P.Behnke, C.A.Kuroita, T.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Renin
A, B
337Homo sapiensMutation(s): 0 
Gene Names: REN
EC: 3.4.23.15
UniProt & NIH Common Fund Data Resources
Find proteins for P00797 (Homo sapiens)
Explore P00797 
Go to UniProtKB:  P00797
PHAROS:  P00797
GTEx:  ENSG00000143839 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00797
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P00797-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6VU
Query on 6VU

Download Ideal Coordinates CCD File 
D [auth A],
R [auth B]
1-(4-methoxybutyl)-~{N}-(2-methylpropyl)-~{N}-[(3~{S},5~{R})-5-morpholin-4-ylcarbonylpiperidin-3-yl]benzimidazole-2-carboxamide
C27 H41 N5 O4
RHIBAIKQWJNESW-YADHBBJMSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
Q [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
E [auth A],
S [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
T [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6VU BindingDB:  5KOT IC50: min: 0.43, max: 1.5 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.203 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.317α = 90
b = 139.317β = 90
c = 139.317γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 6VUClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Structure summary