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 

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

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)
	Binding MOAD:  3KM4	IC50: 1.3 (nM) from 1 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