3GW5

Crystal structure of human renin complexed with a novel inhibitor

PDB DOI: https://doi.org/10.2210/pdb3GW5/pdb

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

Deposited: 2009-03-31 Released: 2009-06-23
Deposition Author(s): Wu, Z., McKeever, B.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.256
R-Value Work: 0.210
R-Value Observed: 0.210

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Design and optimization of renin inhibitors: Orally bioavailable alkyl amines.

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

(2009) Bioorg Med Chem Lett 19: 3541-3545

PubMed: 19457666 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2009.04.140
Primary Citation of Related Structures:
3GW5

PubMed Abstract:
Structure-based drug design led to the identification of a novel class of potent, low MW alkylamine renin inhibitors. Oral administration of lead compound 21l, with MW of 508 and IC(50) of 0.47nM, caused a sustained reduction in mean arterial blood pressure in a double transgenic rat model of hypertension.

Organizational Affiliation

Vitae Pharmaceuticals, 502 West Office Center Drive, Fort Washington, PA 19034, USA. ctice@vitaerx.com

Macromolecule Content

Total Structure Weight: 76.04 kDa
Atom Count: 5,648
Modelled Residue Count: 669
Deposited Residue Count: 674
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00797
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P00797-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
72X Query on 72X Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	(3R)-3-[(1S)-1-(3-chlorophenyl)-1-hydroxy-5-methoxypentyl]-N-{(1S)-2-cyclohexyl-1-[(methylamino)methyl]ethyl}piperidine-1-carboxamide C₂₈ H₄₆ Cl N₃ O₃ LGUUOHMUYOBFQP-MAARLIENSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	E [auth A], F [auth A], G [auth A], H [auth A], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
72X	BindingDB: 3GW5	IC50: min: 0.47, max: 13 (nM) from 3 assay(s)
72X	PDBBind: 3GW5	IC50: 0.47 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.256
R-Value Work: 0.210
R-Value Observed: 0.210
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.203	α = 90
b = 97.069	β = 90
c = 149.546	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
MOLREP	phasing
CNX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-06-23

Deposition Author(s):

Wu, Z.

McKeever, B.M.

Revision History (Full details and data files)

Version 1.0: 2009-06-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
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: 2024-11-20
Changes: Structure summary