7F43

PARP15 catalytic domain in complex with Niraparib

PDB DOI: https://doi.org/10.2210/pdb7F43/pdb

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

Deposited: 2021-06-17 Released: 2022-06-22
Deposition Author(s): Zhou, X.L., Zhou, H., Li, J., Zhang, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.275
R-Value Work: 0.240
R-Value Observed: 0.242

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

PARP15 catalytic domain in complex with Niraparib

Zhou, X.L., Zhou, H., Li, J., Zhang, J.

To be published.

Macromolecule Content

Total Structure Weight: 46.37 kDa
Atom Count: 3,405
Modelled Residue Count: 396
Deposited Residue Count: 400
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein mono-ADP-ribosyltransferase PARP15	A, B	200	Homo sapiens	Mutation(s): 0 Gene Names: PARP15, BAL3 EC: 2.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q460N3 (Homo sapiens) Explore Q460N3 Go to UniProtKB: Q460N3
PHAROS: Q460N3 GTEx: ENSG00000173200
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q460N3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3JD (Subject of Investigation/LOI) Query on 3JD Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide C₁₉ H₂₀ N₄ O PCHKPVIQAHNQLW-CQSZACIVSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
3JD	BindingDB: 7F43	IC50: min: 2.88e+4, max: 2.92e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.275
R-Value Work: 0.240
R-Value Observed: 0.242
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.515	α = 90
b = 68.726	β = 90
c = 160.631	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2022-06-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-06-22
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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.