4QJ1

Co-crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from Cryptosporidium parvum with inhibitor N109

PDB DOI: https://doi.org/10.2210/pdb4QJ1/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Cryptosporidium parvum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-06-03 Released: 2014-08-06
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Hedstrom, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.258
R-Value Work: 0.202
R-Value Observed: 0.205

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Co-crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from Cryptosporidium parvum with inhibitor N109

Kim, Y., Makowska-Grzyska, M., Gu, M., Hedstrom, L., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 157.25 kDa
Atom Count: 10,616
Modelled Residue Count: 1,378
Deposited Residue Count: 1,444
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A, B, C, D	361	Cryptosporidium parvum	Mutation(s): 2 Gene Names: 56k.02, cgd6_20 EC: 1.1.1.205
UniProt
Find proteins for Q8T6T2 (Cryptosporidium parvum) Explore Q8T6T2 Go to UniProtKB: Q8T6T2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8T6T2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
N09 Query on N09 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain N [auth D]	F [auth A], H [auth B], I [auth B], N [auth D]	N-(4-chloro-3-methoxyphenyl)-2-(4-oxochromeno[4,3-c]pyrazol-1(4H)-yl)acetamide C₁₉ H₁₄ Cl N₃ O₄ DJHSRZJOSYWGCG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain N [auth D]
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	E [auth A], G [auth B], K [auth C], M [auth D]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain M [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth D] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth D]	L [auth C], O [auth D], Q [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Focus chain O [auth D] Focus chain Q [auth D] Interactions & Density Focus chain L [auth C] Focus chain O [auth D] Focus chain Q [auth D]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D] mmCIF format, chain P [auth D]	P [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
N09	BindingDB: 4QJ1	IC50: 20 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.258
R-Value Work: 0.202
R-Value Observed: 0.205
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/m34qj1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.412	α = 90
b = 92.337	β = 104.24
c = 91.914	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-08-06

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-08-06
Type: Initial release
Version 1.1: 2017-07-26
Changes: Refinement description, Source and taxonomy
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description