3Q5H

Clinically Useful Alkyl Amine Renin Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3Q5H/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2010-12-28 Released: 2011-11-30 
• Deposition Author(s): Wu, Z., McKeever, B.M.

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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

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

• PubMed: 24900262 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.22 kDa 
• Atom Count: 5,478 
• Modelled Residue Count: 675 
• Deposited Residue Count: 680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Renin	A, B	340	Homo sapiens	Mutation(s): 0  Gene Names: REN, renin 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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P00797-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RX6	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	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
ID	Source	Binding 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 = 54.65	α = 90
b = 97.85	β = 90
c = 149.006	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-30 
Deposition Author(s): Wu, Z., McKeever, B.M.

Revision History  

• 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