8HLR

Human ADP-ribosyltransferase 1 (PARP1) catalytic domain bound to Fluzoparib (SHR3162)

PDB DOI: https://doi.org/10.2210/pdb8HLR/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-11-30 Released: 2024-05-01
Deposition Author(s): Wang, X.Y., Zhou, J., Xu, B.L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.288
R-Value Work: 0.237
R-Value Observed: 0.240

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Human ADP-ribosyltransferase 1 (PARP1) catalytic domain bound to Fluzoparib (SHR3162)

Wang, X.Y., Zhou, J., Xu, B.L.

To be published.

Macromolecule Content

Total Structure Weight: 81.21 kDa
Atom Count: 5,664
Modelled Residue Count: 700
Deposited Residue Count: 708
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 1, processed C-terminus	A, B	354	Homo sapiens	Mutation(s): 1 Gene Names: PARP1, ADPRT, PPOL EC: 2.4.2 (UniProt), 2.4.2.30 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P09874 (Homo sapiens) Explore P09874 Go to UniProtKB: P09874
PHAROS: P09874 GTEx: ENSG00000143799
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09874
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
25I (Subject of Investigation/LOI) Query on 25I Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	Fluzoparib C₂₂ H₁₆ F₄ N₆ O₂ XJGXCBHXFWBOTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
25I	BindingDB: 8HLR	IC50: min: 1.5, max: 10.2 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.288
R-Value Work: 0.237
R-Value Observed: 0.240
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.814	α = 90
b = 92.746	β = 90
c = 164.026	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-01

Deposition Author(s):

Wang, X.Y.

Zhou, J.

Xu, B.L.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82003657
National Natural Science Foundation of China (NSFC)	China	81673300
National Natural Science Foundation of China (NSFC)	China	82173693

Revision History (Full details and data files)

Version 1.0: 2024-05-01
Type: Initial release

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Help and Resources

8HLR

Human ADP-ribosyltransferase 1 (PARP1) catalytic domain bound to Fluzoparib (SHR3162)

Human ADP-ribosyltransferase 1 (PARP1) catalytic domain bound to Fluzoparib (SHR3162)

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)