3K1W | pdb_00003k1w

New Classes of Potent and Bioavailable Human Renin Inhibitors

PDB DOI: https://doi.org/10.2210/pdb3K1W/pdb

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

Deposited: 2009-09-29 Released: 2010-03-02
Deposition Author(s): Prade, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.233 (Depositor), 0.233 (DCC)
R-Value Work:
0.199 (Depositor), 0.198 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

New classes of potent and bioavailable human renin inhibitors

Remen, L., Bezencon, O., Richard-Bildstein, S., Bur, D., Prade, L., Corminboeuf, O., Boss, C., Grisostomi, C., Sifferlen, T., Strickner, P., Hess, P., Delahaye, S., Treiber, A., Weller, T., Binkert, C., Steiner, B., Fischli, W.

(2009) Bioorg Med Chem Lett 19: 6762-6765

PubMed: 19853442 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2009.09.104
Primary Citation Related Structures:
3K1W

PubMed Abstract:
New classes of de novo designed renin inhibitors are reported. Some of these compounds display excellent in vitro and in vivo activities toward human renin in a TGR model. The synthesis of these new types of mono- and bicyclic scaffolds are reported, and properties of selected compounds discussed.

Organizational Affiliation

Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd, CH-4123 Allschwil, Switzerland.

Macromolecule Content

Total Structure Weight: 76.58 kDa
Atom Count: 5,990
Modeled Residue Count: 670
Deposited Residue Count: 682
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Renin	A, B	341	Homo sapiens	Mutation(s): 0 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 A	Go to GlyGen: P00797-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BFX Query on BFX Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	4-{4-[3-(2-bromo-5-fluorophenoxy)propyl]phenyl}-N-(2-chlorobenzyl)-N-cyclopropyl-1,2,5,6-tetrahydropyridine-3-carboxamide C₃₁ H₃₁ Br Cl F N₂ O₂ GNQKDXQPKKYVIX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
HSQ Query on HSQ Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	2-acetylamino-2-deoxy-alpha-L-idopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-SLBCVNJHSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.233 (Depositor), 0.233 (DCC)
R-Value Work: 0.199 (Depositor), 0.198 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.028	α = 90
b = 88.697	β = 90
c = 118.307	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-03-02

Deposition Author(s):

Prade, L.

Revision History (Full details and data files)

Version 1.0: 2010-03-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-11-20
Changes: Data collection, Database references, Structure summary