5TMK | pdb_00005tmk

Optimization of 3,5-Disubstitued Piperidine: Discovery of Non-Peptide mimetics as an Orally Active Renin Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5TMK/pdb

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


• Deposited: 2016-10-13 Released: 2017-10-18 
• Deposition Author(s): Snell, G.P., Behnke, C.A., Okada, K., Hideyuki, O., Sang, B.C., Lane, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.236 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.198 (Depositor) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Optimization of 3,5-Disubstitued Piperidine: Discovery of Non-Peptide mimetics as an Orally Active Renin Inhibitor

Tokuhara, H., Imaeda, Y., Fukase, Y., Iwanaga, K., Taya, N., Watanabe, K., Kanagawa, R., Matsuda, K., Kajimoto, Y., Kusumoto, K., Kondo, M., Snell, G.P., Behnke, C.A., Kuroita, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75.49 kDa 
• Atom Count: 5,121 
• Modeled Residue Count: 663 
• Deposited Residue Count: 674 
• Unique protein chains: 1

Macromolecules

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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P00797-1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7EJ	D [auth A], H [auth B]	1-(4-methoxybutyl)-N-(2-methylpropyl)-N-[(3S,5R)-5-(morpholine-4-carbonyl)piperidin-3-yl]-5-phenyl-1H-pyrrole-2-carboxamide C30 H44 N4 O4 URICGOHQZDVMJG-FTJBHMTQSA-N
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG	I [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS	E [auth A], F [auth A], G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.236 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.198 (Depositor) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.717	α = 90
b = 139.717	β = 90
c = 139.717	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-18 
Deposition Author(s): Snell, G.P., Behnke, C.A., Okada, K., Hideyuki, O., Sang, B.C., Lane, W.

Revision History  

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Structure summary