4GJA | pdb_00004gja

Crystal structure of renin in complex with NVP-AYL747 (compound 5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.230 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4GJA

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

A novel class of oral direct Renin inhibitors: highly potent 3,5-disubstituted piperidines bearing a tricyclic p3-p1 pharmacophore.

Ostermann, N.Ruedisser, S.Ehrhardt, C.Breitenstein, W.Marzinzik, A.Jacoby, E.Vangrevelinghe, E.Ottl, J.Klumpp, M.Hartwieg, J.C.Cumin, F.Hassiepen, U.Trappe, J.Sedrani, R.Geisse, S.Gerhartz, B.Richert, P.Francotte, E.Wagner, T.Kromer, M.Kosaka, T.Webb, R.L.Rigel, D.F.Maibaum, J.Baeschlin, D.K.

(2013) J Med Chem 56: 2196-2206

  • DOI: https://doi.org/10.1021/jm301706j
  • Primary Citation Related Structures: 
    4GJ8, 4GJ9, 4GJA, 4GJB, 4GJC, 4GJD

  • PubMed Abstract: 

    A small library of fragments comprising putative recognition motifs for the catalytic dyad of aspartic proteases was generated by in silico similarity searches within the corporate compound deck based on rh-renin active site docking and scoring filters. Subsequent screening by NMR identified the low-affinity hits 3 and 4 as competitive active site binders, which could be shown by X-ray crystallography to bind to the hydrophobic S3-S1 pocket of rh-renin. As part of a parallel multiple hit-finding approach, the 3,5-disubstituted piperidine (rac)-5 was discovered by HTS using a enzymatic assay. X-ray crystallography demonstrated the eutomer (3S,5R)-5 to be a peptidomimetic inhibitor binding to a nonsubstrate topography of the rh-renin prime site. The design of the potent and selective (3S,5R)-12 bearing a P3(sp)-tethered tricyclic P3-P1 pharmacophore derived from 3 is described. (3S,5R)-12 showed oral bioavailability in rats and demonstrated blood pressure lowering activity in the double-transgenic rat model.


  • Organizational Affiliation
    • Novartis Pharma AG, Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 76.22 kDa 
  • Atom Count: 5,522 
  • Modeled Residue Count: 674 
  • Deposited Residue Count: 680 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Renin
A, B
340Homo 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0M3

Query on 0M3



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
(3S,5R)-N-(2,2-diphenylethyl)-5-{[(4-methylphenyl)sulfonyl]amino}piperidine-3-carboxamide
C27 H31 N3 O3 S
TUYPQRDSHLXMFM-BJKOFHAPSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
0M3 BindingDB:  4GJA IC50: 1200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.230 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.556α = 90
b = 141.556β = 90
c = 141.556γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-04-10
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-11-06
    Changes: Structure summary