2IGY | pdb_00002igy

Achiral, Cheap and Potent Inhibitors of Plasmepsins II

PDB DOI: https://doi.org/10.2210/pdb2IGY/pdb

Classification: HYDROLASE
Organism(s): Plasmodium falciparum
Mutation(s): No

Deposited: 2006-09-25 Released: 2006-11-28
Deposition Author(s): Prade, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.264 (Depositor), 0.218 (DCC)
R-Value Work:
0.211 (Depositor), 0.211 (DCC)
R-Value Observed:
0.214 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Achiral, Cheap, and Potent Inhibitors of Plasmepsins I, II, and IV.

Boss, C., Corminboeuf, O., Grisostomi, C., Meyer, S., Jones, A.F., Prade, L., Binkert, C., Fischli, W., Weller, T., Bur, D.

(2006) ChemMedChem 1: 1341-1345

PubMed: 17091526 Search on PubMed
DOI: https://doi.org/10.1002/cmdc.200600223
Primary Citation Related Structures:
2IGX, 2IGY

Organizational Affiliation

Drug Discovery, Chemistry and Biology, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, 4123 Allschwil, Switzerland.

Macromolecule Content

Total Structure Weight: 74.99 kDa
Atom Count: 5,368
Modeled Residue Count: 658
Deposited Residue Count: 658
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasmepsin-2	A, B	329	Plasmodium falciparum	Mutation(s): 0 EC: 3.4.23.39
UniProt
Find proteins for P46925 (Plasmodium falciparum (isolate HB3)) Explore P46925 Go to UniProtKB: P46925
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46925
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A2T Query on A2T Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	N-[1-(3-METHYLBUTYL)PIPERIDIN-4-YL]-N-{4-[METHYL(PYRIDIN-4-YL)AMINO]BENZYL}-4-PENTYLBENZAMIDE C₃₅ H₄₈ N₄ O WRFRQUOWNCJODU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
A2T	BindingDB: 2IGY	IC50: 113 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.264 (Depositor), 0.218 (DCC)
R-Value Work: 0.211 (Depositor), 0.211 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.099	α = 90
b = 161.099	β = 90
c = 73.932	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-11-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-11-28
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.