3Q3T

Alkyl Amine Renin Inhibitors: Filling S1 from S3

PDB DOI: https://doi.org/10.2210/pdb3Q3T/pdb

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

Deposited: 2010-12-22 Released: 2011-08-03
Deposition Author(s): Wu, Z., McKeever, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.268 (Depositor), 0.270 (DCC)
R-Value Work:
0.200 (Depositor), 0.210 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

Literature

Biphenyl/diphenyl ether renin inhibitors: Filling the S1 pocket of renin via the S3 pocket.

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

(2011) Bioorg Med Chem Lett 21: 4836-4843

PubMed: 21741239 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2011.06.043
Primary Citation of Related Structures:
3Q3T

PubMed Abstract:
Structure-based design led to the discovery of a novel class of renin inhibitors in which an unprecedented phenyl ring filling the S1 site is attached to the phenyl ring filling the S3 pocket. Optimization for several parameters including potency in the presence of human plasma, selectivity against CYP3A4 inhibition and improved rat oral bioavailability led to the identification of 8d which demonstrated antihypertensive efficacy in a transgenic rat model of human hypertension.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 76.33 kDa
Atom Count: 5,428
Modelled Residue Count: 670
Deposited Residue Count: 680
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Renin	A, B	340	Homo sapiens	Mutation(s): 0 Gene Names: REN, renin 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 LOADING

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RX0 Query on RX0 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	[(1S,3R,4S)-3-amino-4-hydroxycyclopentyl]{(3R)-3-[(1S)-1-(biphenyl-2-yl)-1-hydroxy-5-methoxypentyl]piperidin-1-yl}methanone C₂₉ H₄₀ N₂ O₄ GBAKDRIJFSDCNN-YJFNBJRFSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
RX0	BindingDB: 3Q3T	IC50: 37 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.268 (Depositor), 0.270 (DCC)
R-Value Work: 0.200 (Depositor), 0.210 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.253	α = 90
b = 97.585	β = 90
c = 148.651	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-03

Deposition Author(s):

Wu, Z.

McKeever, B.

Revision History (Full details and data files)

Version 1.0: 2011-08-03
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2021-03-31
Changes: Source and taxonomy, Structure summary
Version 2.2: 2023-09-13
Changes: Data collection, Database references, Refinement description
Version 2.3: 2024-10-30
Changes: Structure summary