7ALE | pdb_00007ale

Crystal structure of human PAICS in complex with inhibitor 69

PDB DOI: https://doi.org/10.2210/pdb7ALE/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-10-06 Released: 2022-04-20
Deposition Author(s): Skerlova, J., Marttila, P., Unterlass, J., Jemth, A.-S., Henriksson, M., Wakchaure, P., Grube, M., Warpman Berglund, U., Homan, E., Helleday, T., Stenmark, P.
Funding Organization(s): Swedish Research Council, European Research Council (ERC), European Regional Development Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.261 (Depositor), 0.270 (DCC)
R-Value Work:
0.225 (Depositor), 0.230 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Cellular and biochemical validation of a potent PAICS inhibitor

Marttila, P., Skerlova, J., Unterlass, J., Jemth, A.-S., Henriksson, M., Wakchaure, P., Grube, M., Warpman Berglund, U., Homan, E., Stenmark, P., Helleday, T.

To be published.

Macromolecule Content

Total Structure Weight: 96.21 kDa
Atom Count: 6,650
Modeled Residue Count: 838
Deposited Residue Count: 850
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multifunctional protein ADE2	A, B	425	Homo sapiens	Mutation(s): 0 Gene Names: PAICS, ADE2, AIRC, PAIS EC: 6.3.2.6 (PDB Primary Data), 4.1.1.21 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P22234 (Homo sapiens) Explore P22234 Go to UniProtKB: P22234
PHAROS: P22234 GTEx: ENSG00000128050
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22234
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RLK (Subject of Investigation/LOI) Query on RLK Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	2-azanyl-~{N}-[2-bromanyl-5-[4-[3-(dimethylamino)propylsulfonyl]piperazin-1-yl]phenyl]-1,3-oxazole-4-carboxamide C₁₉ H₂₇ Br N₆ O₄ S GTJMWLKWMPRNKA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
OK8 (Subject of Investigation/LOI) Query on OK8 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	(2~{S})-2-[[5-azanyl-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]imidazol-4-yl]car bonylamino]butanedioic acid C₁₃ H₁₉ N₄ O₁₂ P NAQGHJTUZRHGAC-ZZZDFHIKSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
RLK	BindingDB: 7ALE	IC50: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.261 (Depositor), 0.270 (DCC)
R-Value Work: 0.225 (Depositor), 0.230 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.772	α = 90
b = 152.44	β = 90
c = 222.755	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-04-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2015-00162
Swedish Research Council	Sweden	2018-03406
European Research Council (ERC)	European Union	TAROX-695376
European Regional Development Fund	European Union	CZ.02.2.69/0.0/0.0/16_027/0008477