5KOS | pdb_00005kos

Discovery of TAK-272: A Novel, Potent and Orally Active Renin In-hibitor

PDB DOI: https://doi.org/10.2210/pdb5KOS/pdb

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

Deposited: 2016-07-01 Released: 2016-11-16
Deposition Author(s): Snell, G.P., Behnke, C.A., Okada, K., Hideyuki, O., Sang, B.-C., Lane, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.230 (Depositor), 0.227 (DCC)
R-Value Work:
0.185 (Depositor)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of TAK-272: A Novel, Potent, and Orally Active Renin Inhibitor.

Imaeda, Y., Tokuhara, H., Fukase, Y., Kanagawa, R., Kajimoto, Y., Kusumoto, K., Kondo, M., Snell, G., Behnke, C.A., Kuroita, T.

(2016) ACS Med Chem Lett 7: 933-938

PubMed: 27774132 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.6b00251
Primary Citation Related Structures:
5KOS

PubMed Abstract:
The aspartic proteinase renin is an attractive target for the treatment of hypertension and cardiovascular/renal disease such as chronic kidney disease and heart failure. We introduced an S1' site binder into the lead compound 1 guided by structure-based drug design (SBDD), and further optimization of physicochemical properties led to the discovery of benzimidazole derivative 10 (1-(4-methoxybutyl)- N -(2-methylpropyl)- N -[(3 S ,5 R )-5-(morpholin-4-yl)carbonylpiperidin-3-yl]-1 H- benzimidazole-2-carboxamide hydrochloride, TAK-272) as a highly potent and orally active renin inhibitor. Compound 10 demonstrated good oral bioavailability (BA) and long-lasting efficacy in rats. Compound 10 is currently in clinical trials.

Organizational Affiliation

Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.

Macromolecule Content

Total Structure Weight: 76.46 kDa
Atom Count: 5,472
Modeled Residue Count: 663
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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6VS Query on 6VS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain P [auth B] mmCIF format, chain D [auth A] mmCIF format, chain P [auth B]	D [auth A], P [auth B]	2-~{tert}-butyl-4-(3-methoxypropylamino)-~{N}-(2-methylpropyl)-~{N}-[(3~{S},5~{R})-5-morpholin-4-ylcarbonylpiperidin-3-yl]pyrimidine-5-carboxamide C₂₇ H₄₆ N₆ O₄ ISBMTDVOSWIALV-RTWAWAEBSA-N		Interactions Focus chain D [auth A] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain P [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain O [auth B]	C [auth A], O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain O [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B]	M [auth A], N [auth A], Q [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B]
DMS Query on DMS 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 I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain S [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 I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [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 I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], R [auth B], S [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-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 I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [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 I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
6VS	BindingDB: 5KOS	IC50: min: 0.38, max: 1.5 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.230 (Depositor), 0.227 (DCC)
R-Value Work: 0.185 (Depositor)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.077	α = 90
b = 137.077	β = 90
c = 137.077	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-11-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-11-16
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Structure summary

5KOS | pdb_00005kos

Discovery of TAK-272: A Novel, Potent and Orally Active Renin In-hibitor

Literature

Discovery of TAK-272: A Novel, Potent, and Orally Active Renin Inhibitor.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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