5VRP | pdb_00005vrp

Crystal Structure of Human Renin in Complex with a biphenylpipderidinylcarbinol

PDB DOI: https://doi.org/10.2210/pdb5VRP/pdb

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

Deposited: 2017-05-11 Released: 2017-10-18
Deposition Author(s): Concha, N., Zhao, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.22 Å
R-Value Free:
0.262 (Depositor), 0.265 (DCC)
R-Value Work:
0.245 (Depositor), 0.246 (DCC)
R-Value Observed:
0.246 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Discovery of renin inhibitors containing a simple aspartate binding moiety that imparts reduced P450 inhibition.

Lawhorn, B.G., Tran, T., Hong, V.S., Morgan, L.A., Le, B.T., Harpel, M.R., Jolivette, L., Diaz, E., Schwartz, B., Gross, J.W., Tomaszek, T., Semus, S., Concha, N., Smallwood, A., Holt, D.A., Kallander, L.S.

(2017) Bioorg Med Chem Lett 27: 4838-4843

PubMed: 28985999 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2017.09.046
Primary Citation Related Structures:
5V8V, 5VPM, 5VRP

PubMed Abstract:
Discovery of potent renin inhibitors which contain a simplified alkylamino Asp-binding group and exhibit improved selectivity for renin over Cyp3A4 is described. Structure-function results in this series are rationalized based on analysis of selected compounds bound to renin, and the contribution of each molecular feature leading to the reduced P450 inhibition is quantified.

Organizational Affiliation

Heart Failure DPU, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA 19406, USA. Electronic address: brian.2.lawhorn@gsk.com.

Macromolecule Content

Total Structure Weight: 76.54 kDa
Atom Count: 5,207
Modeled Residue Count: 666
Deposited Residue Count: 674
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00797
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B	Go to GlyGen: P00797-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9JD Query on 9JD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	E [auth A], F [auth A], H [auth B], I [auth B]	methyl [(4S)-4-{(3R)-1-[(3S)-4-amino-3-hydroxybutanoyl]piperidin-3-yl}-4-(3'-ethyl-6-fluoro[1,1'-biphenyl]-2-yl)-4-hydroxybutyl]carbamate C₂₉ H₄₀ F N₃ O₅ IIIBTAZKWKWKNG-AFKLWXAFSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.22 Å
R-Value Free: 0.262 (Depositor), 0.265 (DCC)
R-Value Work: 0.245 (Depositor), 0.246 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.334	α = 90
b = 99.933	β = 90
c = 146.529	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-10-18

Deposition Author(s):

Concha, N.

Zhao, B.

Revision History (Full details and data files)

Version 1.0: 2017-10-18
Type: Initial release
Version 1.1: 2017-10-25
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Structure summary