8VOF

GI targeted CpPI4K inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8VOF/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): Yes 


• Deposited: 2024-01-15 Released: 2024-09-04 
• Deposition Author(s): Knapp, M.S., Cuellar, C., Mamo, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.270 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 

Starting Model: experimental

Literature

Cryptosporidium PI(4)K inhibitor EDI048 is a gut-restricted parasiticidal agent to treat paediatric enteric cryptosporidiosis

Manjunatha, U.H., Diagana, T.T.

(2024) Nat Microbiol 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 86.23 kDa 
• Atom Count: 4,947 
• Modelled Residue Count: 644 
• Deposited Residue Count: 745 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Phosphatidylinositol 4-kinase beta,Isoform 2 of Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta	A	529	Homo sapiens	Mutation(s): 2  Gene Names: PI4KB, PIK4CB EC: 2.7.1.67
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBF8 (Homo sapiens) Explore Q9UBF8  Go to UniProtKB:  Q9UBF8
PHAROS:  Q9UBF8 GTEx:  ENSG00000143393

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-11A	B	216	Homo sapiens	Mutation(s): 1  Gene Names: RAB11A, RAB11 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P62491 (Homo sapiens) Explore P62491  Go to UniProtKB:  P62491
PHAROS:  P62491 GTEx:  ENSG00000103769

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ADE (Subject of Investigation/LOI)	C [auth A]	methyl 2-chloro-5-(methyl{(8R)-3-[4-(methylcarbamoyl)phenyl]pyrazolo[1,5-a]pyridine-5-carbonyl}amino)benzoate C25 H21 Cl N4 O4 UUGWSUYPJGPKKF-UHFFFAOYSA-N
GDP	E [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.270 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.57	α = 90
b = 105.224	β = 90
c = 186.423	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Knapp, M.S., Cuellar, C., Mamo, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release
  
• Version 1.1: 2024-09-25
  Changes: Database references