7MLK

Crystal structure of human PI3Ka (p110a subunit) with MMV085400 bound to the active site determined at 2.9 angstroms resolution

• PDB DOI: https://doi.org/10.2210/pdb7MLK/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2021-04-28 Released: 2022-05-04 
• Deposition Author(s): Krake, S.H., Martinez, P.D.G., Poggi, M.L., Ferreira, M.S., Aguiar, A.C.C., Souza, G.E., Wenlock, M., Jones, B., Steinbrecher, T., Day, T., McPhail, J., Burke, J., Yeo, T., Mok, S., Uhlemann, A.C., Fidock, D.A., Chen, P., Grodsky, N., Deng, Y.L., Guido, R.V.C., Campbell, S.F., Willis, P.A., Dias, L.C.
• Funding Organization(s): Other private

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.242 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

Discovery of 2,6-disubstituted pyrazines as potent PI4K inhibitors with antimalarial activity

Krake, S.H., Martinez, P.D.G., Poggi, M.L., Ferreira, M.S., Aguiar, A.C.C., Souza, G.E., Wenlock, M., Jones, B., Steinbrecher, T., Day, T., McPhail, J., Burke, J., Yeo, T., Mok, S., Uhlemann, A.C., Fidock, D.A., Chen, P., Grodsky, N., Deng, Y.L., Guido, R.V.C., Campbell, S.F., Willis, P.A., Dias, L.C.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 113 kDa 
• Atom Count: 7,270 
• Modelled Residue Count: 888 
• Deposited Residue Count: 968 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A	968	Homo sapiens	Mutation(s): 0  Gene Names: PIK3CA EC: 2.7.1.137 (PDB Primary Data), 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens) Explore P42336  Go to UniProtKB:  P42336
PHAROS:  P42336 GTEx:  ENSG00000121879

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZHY (Subject of Investigation/LOI)	B [auth A]	4-[6-(3,4,5-trimethoxyanilino)pyrazin-2-yl]benzamide C20 H20 N4 O4 LZLKDDDQYGMZTB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.242 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.849	α = 90
b = 134.794	β = 90
c = 141.95	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
BUSTER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-04 
Deposition Author(s): Krake, S.H., Martinez, P.D.G., Poggi, M.L., Ferreira, M.S., Aguiar, A.C.C., Souza, G.E., Wenlock, M., Jones, B., Steinbrecher, T., Day, T., McPhail, J., Burke, J., Yeo, T., Mok, S., Uhlemann, A.C., Fidock, D.A., Chen, P., Grodsky, N., Deng, Y.L., Guido, R.V.C., Campbell, S.F., Willis, P.A., Dias, L.C.

---

Funding Organization	Location	Grant Number
Other private	Brazil	RD-12-0103

Revision History  

• Version 1.0: 2022-05-04
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description