5VRP

Crystal Structure of Human Renin in Complex with a biphenylpipderidinylcarbinol

• PDB DOI: https://doi.org/10.2210/pdb5VRP/pdb

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


• Deposited: 2017-05-11 Released: 2017-10-18 
• Deposition Author(s): Concha, N., Zhao, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.22 Å
• R-Value Free: 0.262 
• R-Value Work: 0.245 
• R-Value Observed: 0.246 

Literature

Discovery of renin inhibitors containing a simple aspartate binding moiety that imparts reduced P450 inhibition.

Lawhorn, B.G., Tran, T., Hong, V.S., Morgan, L.A., Le, B.T., Harpel, M.R., Jolivette, L., Diaz, E., Schwartz, B., Gross, J.W., Tomaszek, T., Semus, S., Concha, N., Smallwood, A., Holt, D.A., Kallander, L.S.

(2017) Bioorg Med Chem Lett 27: 4838-4843

• PubMed: 28985999 
• DOI: https://doi.org/10.1016/j.bmcl.2017.09.046
• Primary Citation of Related Structures:  
  5V8V, 5VPM, 5VRP


• PubMed Abstract: 
  

  Discovery of potent renin inhibitors which contain a simplified alkylamino Asp-binding group and exhibit improved selectivity for renin over Cyp3A4 is described. Structure-function results in this series are rationalized based on analysis of selected compounds bound to renin, and the contribution of each molecular feature leading to the reduced P450 inhibition is quantified.

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Organizational Affiliation: 

Heart Failure DPU, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA 19406, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.54 kDa 
• Atom Count: 5,207 
• Modelled Residue Count: 666 
• Deposited Residue Count: 674 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Renin	A, B	337	Homo sapiens	Mutation(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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P00797-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9JD	E [auth A], F [auth A], H [auth B], I [auth B]	methyl [(4S)-4-{(3R)-1-[(3S)-4-amino-3-hydroxybutanoyl]piperidin-3-yl}-4-(3'-ethyl-6-fluoro[1,1'-biphenyl]-2-yl)-4-hydroxybutyl]carbamate C29 H40 F N3 O5 IIIBTAZKWKWKNG-AFKLWXAFSA-N
NAG	C [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.22 Å
• R-Value Free: 0.262 
• R-Value Work: 0.245 
• R-Value Observed: 0.246 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.334	α = 90
b = 99.933	β = 90
c = 146.529	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-18 
Deposition Author(s): Concha, N., Zhao, B.

Revision History  

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary