7PWD | pdb_00007pwd

Structure of an inhibited GRK2-G-beta and G-gamma complex

PDB DOI: https://doi.org/10.2210/pdb7PWD/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens, Bos taurus
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2021-10-06 Released: 2021-10-20
Deposition Author(s): Faucher, N., Tauchert, M.J., Konz Makino, D.L., Vuillard, L.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.230 (Depositor), 0.231 (DCC)
R-Value Work:
0.192 (Depositor), 0.195 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Synthesis of thieno[2,3-c]pyridine derived GRK2 inhibitors

Balo, T., Sapi, A., Kiss, A., Raimbaud, E., Paysant, J., Cattin, M.E., Berger, S., Kotschy, A., Faucher, N.

(2022) Monatsh Chem

DOI: https://doi.org/10.1007/s00706-021-02889-2

Macromolecule Content

Total Structure Weight: 127.49 kDa
Atom Count: 8,410
Modeled Residue Count: 1,023
Deposited Residue Count: 1,114
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-adrenergic receptor kinase 1	A	697	Homo sapiens	Mutation(s): 1 Gene Names: GRK2, ADRBK1, BARK, BARK1 EC: 2.7.11.15
UniProt & NIH Common Fund Data Resources
Find proteins for P25098 (Homo sapiens) Explore P25098 Go to UniProtKB: P25098
PHAROS: P25098 GTEx: ENSG00000173020
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25098
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	340	Bos taurus	Mutation(s): 0 Gene Names: GNB1
UniProt
Find proteins for P62871 (Bos taurus) Explore P62871 Go to UniProtKB: P62871
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62871
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C [auth G]	77	Bos taurus	Mutation(s): 1 Gene Names: GNG2
UniProt
Find proteins for P63212 (Bos taurus) Explore P63212 Go to UniProtKB: P63212
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63212
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8DS (Subject of Investigation/LOI) Query on 8DS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	4-chloranyl-N-[2-(4-chlorophenyl)ethyl]thieno[2,3-c]pyridine-2-carboxamide C₁₆ H₁₂ Cl₂ N₂ O S QRJZINDCUNBUGT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.230 (Depositor), 0.231 (DCC)
R-Value Work: 0.192 (Depositor), 0.195 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.6	α = 90
b = 74.549	β = 115.31
c = 123.411	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-10-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2021-10-20
Type: Initial release
Version 1.1: 2022-05-18
Changes: Database references, Refinement description
Version 1.2: 2024-06-19
Changes: Data collection, Database references