3VYD

Human renin in complex with inhibitor 6

• PDB DOI: https://doi.org/10.2210/pdb3VYD/pdb

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


• Deposited: 2012-09-24 Released: 2012-12-19 
• Deposition Author(s): Takahashi, M., Hanzawa, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.282 
• R-Value Work: 0.203 
• R-Value Observed: 0.211 

Starting Model: experimental

Literature

Design and discovery of new (3S,5R)-5-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]piperidine-3-carboxamides as potent renin inhibitors

Mori, Y., Ogawa, Y., Mochizuki, A., Nakamura, Y., Sugita, C., Miyazaki, S., Tamaki, K., Matsui, Y., Takahashi, M., Nagayama, T., Nagai, Y., Inoue, S., Nishi, T.

(2012) Bioorg Med Chem Lett 22: 7677-7682

• PubMed: 23122821 
• DOI: https://doi.org/10.1016/j.bmcl.2012.09.103
• Primary Citation of Related Structures:  
  3VYD, 3VYE, 3VYF


• PubMed Abstract: 
  

  Utilizing X-ray crystal structure analysis, (3S,5R)-5-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]piperidine-3-carboxamides were designed and identified as renin inhibitors. The most potent compound 15 demonstrated favorable pharmacokinetic and pharmacodynamic profiles in rat.

---

Organizational Affiliation: 

Lead Discovery & Optimization Research Laboratories I, 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: 75.87 kDa 
• Atom Count: 5,455 
• Modelled Residue Count: 674 
• 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
GTEx:  ENSG00000143839
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P00797-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VYD	D [auth A], F [auth B]	(3S,5R)-5-{[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]methyl}-N-(3-methylbutyl)piperidine-3-carboxamide C24 H37 Cl N4 O2 XGYKQWJDBJCEAW-MOPGFXCFSA-N
NAG	C [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VYD	BindingDB:  3VYD	IC50: min: 406, max: 1000 (nM) from 2 assay(s)
	PDBBind:  3VYD	IC50: 406 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.282 
• R-Value Work: 0.203 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.025	α = 90
b = 141.025	β = 90
c = 141.025	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-19 
Deposition Author(s): Takahashi, M., Hanzawa, H.

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary