3Q5H

Clinically Useful Alkyl Amine Renin Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Discovery of VTP-27999, an Alkyl Amine Renin Inhibitor with Potential for Clinical Utility.

Jia, L.Simpson, R.D.Yuan, J.Xu, Z.Zhao, W.Cacatian, S.Tice, C.M.Guo, J.Ishchenko, A.Singh, S.B.Wu, Z.McKeever, B.M.Bukhtiyarov, Y.Johnson, J.A.Doe, C.P.Harrison, R.K.McGeehan, G.M.Dillard, L.W.Baldwin, J.J.Claremon, D.A.

(2011) ACS Med Chem Lett 2: 747-751

  • DOI: https://doi.org/10.1021/ml200137x
  • Primary Citation of Related Structures:  
    3Q4B, 3Q5H

  • PubMed Abstract: 

    Structure guided optimization of a series of nonpeptidic alkyl amine renin inhibitors allowed the rational incorporation of additional polar functionality. Replacement of the cyclohexylmethyl group occupying the S1 pocket with a (R)-(tetrahydropyran-3-yl)methyl group and utilization of a different attachment point led to the identification of clinical candidate 9. This compound demonstrated excellent selectivity over related and unrelated off-targets, >15% oral bioavailability in three species, oral efficacy in a double transgenic rat model of hypertension, and good exposure in humans.


  • Organizational Affiliation

    Vitae Pharmaceuticals, 502 West Office Center Drive, Fort Washington, Pennsylvania 19034, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Renin
A, B
340Homo sapiensMutation(s): 0 
Gene Names: RENrenin
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
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RX6
Query on RX6

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
methyl (2-{(R)-(3-chlorophenyl)[(3R)-1-({(2S)-1-(methylamino)-3-[(3R)-tetrahydro-2H-pyran-3-yl]propan-2-yl}carbamoyl)piperidin-3-yl]methoxy}ethyl)carbamate
C26 H41 Cl N4 O5
GCNDDOJRCKHYLZ-ZXMXYHOLSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth B]
D [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth B],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
RX6 PDBBind:  3Q5H IC50: 560 (nM) from 1 assay(s)
BindingDB:  3Q5H IC50: min: 0.42, max: 0.56 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.65α = 90
b = 97.85β = 90
c = 149.006γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary