5SZ9

Structure-based design of a new series of N-piperidin-3-ylpyrimidine-5-carboxamides as renin inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Renin
A, B
339Homo 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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
74Y
Query on 74Y

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
(azepan-1-yl)(2-{[(furan-2-yl)methyl]amino}-6-methylpyridin-3-yl)methanone
C18 H23 N3 O2
JCTPWJNVLSRFOU-UHFFFAOYSA-N
NAG
Query on NAG

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

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
K [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
74Y BindingDB:  5SZ9 IC50: 3.80e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.129α = 90
b = 140.129β = 90
c = 140.129γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary