3KM4

Optimization of Orally Bioavailable Alkyl Amine Renin Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3KM4/pdb

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


• Deposited: 2009-11-09 Released: 2010-01-12 
• Deposition Author(s): Wu, Z., McKeever, B.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.261 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Starting Model: experimental

Literature

Optimization of orally bioavailable alkyl amine renin inhibitors.

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

(2010) Bioorg Med Chem Lett 20: 694-699

• PubMed: 19959358 
• DOI: https://doi.org/10.1016/j.bmcl.2009.11.066
• Primary Citation of Related Structures:  
  3KM4


• PubMed Abstract: 
  

  Structure-guided drug design led to new alkylamine renin inhibitors with improved in vitro and in vivo potency. Lead compound 21a, has an IC(50) of 0.83nM for the inhibition of human renin in plasma (PRA). Oral administration of 21a at 10mg/kg resulted in >20h reduction of blood pressure in a double transgenic rat model of hypertension.

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Organizational Affiliation: 

Vitae Pharmaceuticals, 502 West Office Center Drive, Fort Washington, PA 19034, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.61 kDa 
• Atom Count: 5,815 
• Modelled Residue Count: 670 
• 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: HUMAN_RENIN, 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

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
22X	D [auth A], E [auth A], G [auth B], H [auth B]	(3R)-3-[(1S)-4-(acetylamino)-1-(3-chlorophenyl)-1-hydroxybutyl]-N-{(1S)-2-cyclohexyl-1-[(methylamino)methyl]ethyl}piperidine-1-carboxamide C28 H45 Cl N4 O3 PPGUIDOUTGLYCO-MAARLIENSA-N
NAG	F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
22X	BindingDB:  3KM4	IC50: min: 1.3, max: 16 (nM) from 2 assay(s)
	PDBBind:  3KM4	IC50: 1.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.261 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.834	α = 90
b = 96.94	β = 90
c = 148.568	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Wu, Z., McKeever, B.M.

Revision History  

• Version 1.0: 2010-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-06-19
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Structure summary