3VUC | pdb_00003vuc

Human renin in complex with compound 5

• PDB DOI: https://doi.org/10.2210/pdb3VUC/pdb

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


• Deposited: 2012-06-26 Released: 2013-05-15 
• Deposition Author(s): Takahashi, M., Matsui, Y., Hanzawa, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Discovery of DS-8108b, a Novel Orally Bioavailable Renin Inhibitor.

Nakamura, Y., Fujimoto, T., Ogawa, Y., Sugita, C., Miyazaki, S., Tamaki, K., Takahashi, M., Matsui, Y., Nagayama, T., Manabe, K., Mizuno, M., Masubuchi, N., Chiba, K., Nishi, T.

(2012) ACS Med Chem Lett 3: 754-758

• PubMed: 24900544 
• DOI: https://doi.org/10.1021/ml300168e
• Primary Citation Related Structures: 
  3VUC


• PubMed Abstract: 
  

  A novel orally bioavailable renin inhibitor, DS-8108b (5), showing potent renin inhibitory activity and excellent in vivo efficacy is described. We report herein the synthesis and pharmacological effects of 5 including renin inhibitory activity in vitro, suppressive effects of ex vivo plasma renin activity (PRA) in cynomolgus monkey, pharmacokinetic data, and blood pressure-lowering effects in an animal model. Compound 5 demonstrated inhibitory activities toward human renin (IC50 = 0.9 nM) and human and monkey PRA (IC50 = 1.9 and 6.3 nM, respectively). Oral administration of single doses of 3 and 10 mg/kg of 5 in cynomolgus monkey on pretreatment with furosemide led to dose-dependent significant reductions in ex vivo PRA and sustained lowering of mean arterial blood pressure for more than 12 h.

---

Organizational Affiliation: 
• Lead Discovery & Optimization Research Laboratories I, Lead Discovery & Optimization Research Laboratories II, Cardiovascular-Metabolics Research Laboratories, Biological Research Laboratories, Drug Metabolism & Pharmacokinetics Research Laboratories, and Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd. , 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan.

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.

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 76.1 kDa 
• Atom Count: 5,543 
• Modeled Residue Count: 678 
• 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 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HHE	D [auth A], F [auth B]	(2R,4S,5S)-5-amino-6-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]-2-ethyl-4-hydroxy-N-[(1R,2S,3S,5S,7S)-5-hydroxytricyclo[3.3.1.1~3,7~]dec-2-yl]hexanamide C30 H45 Cl N4 O4 MGQQKSSUXHKDSK-PTMRNKDMSA-N
NAG	C [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.289	α = 90
b = 141.289	β = 90
c = 141.289	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-15 
Deposition Author(s): Takahashi, M., Matsui, Y., Hanzawa, H.

Revision History  

• Version 1.0: 2013-05-15
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2019-12-25
  Changes: Database references, Derived calculations
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-10-30
  Changes: Structure summary