6NFG

CYCLIC GMP-AMP SYNTHASE in complex with compound 16 inhibitor: 7-hydroxy-N-methyl-5-phenylpyrazolo[1,5-a]pyrimidine-3-carboxamide

PDB DOI: https://doi.org/10.2210/pdb6NFG/pdb
Entry: 6NFG supersedes: 5V8H

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-12-20 Released: 2019-01-23
Deposition Author(s): Hall, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free: 0.244
R-Value Work: 0.182
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

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

Literature

Discovery of a high affinity inhibitor of cGAS

Hall, J.

To be published.

Macromolecule Content

Total Structure Weight: 85.48 kDa
Atom Count: 5,598
Modelled Residue Count: 694
Deposited Residue Count: 724
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIC GMP-AMP SYNTHASE	A, B	362	Homo sapiens	Mutation(s): 0 Gene Names: CGAS, C6orf150, MB21D1 EC: 2.7.7.86
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N884 (Homo sapiens) Explore Q8N884 Go to UniProtKB: Q8N884
PHAROS: Q8N884 GTEx: ENSG00000164430
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N884
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KKP Query on KKP 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]	D [auth A], F [auth B]	7-hydroxy-N-methyl-5-phenylpyrazolo[1,5-a]pyrimidine-3-carboxamide C₁₄ H₁₂ N₄ O₂ RUSORFYZKCLNDR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ZN Query on ZN 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]	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-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]

Binding Affinity Annotations
ID	Source	Binding Affinity
KKP	BindingDB: 6NFG	Kd: 7.80e+4 (nM) from 1 assay(s)
KKP	BindingDB: 6NFG	IC50: min: 6.90e+4, max: 1.25e+5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free: 0.244
R-Value Work: 0.182
R-Value Observed: 0.185
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 217.148	α = 90
b = 45.602	β = 105.69
c = 86.82	γ = 90

Software Package:

Software Name	Purpose
Aimless	data reduction
Aimless	data scaling
REFMAC	phasing
BUSTER	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-01-23

Deposition Author(s):

Hall, J.

This entry supersedes: 5V8H

Revision History (Full details and data files)

Version 1.0: 2019-01-23
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references

Prepare Data

Validate Data

Deposit Data

Help and Resources

6NFG

CYCLIC GMP-AMP SYNTHASE in complex with compound 16 inhibitor: 7-hydroxy-N-methyl-5-phenylpyrazolo[1,5-a]pyrimidine-3-carboxamide

Discovery of a high affinity inhibitor of cGAS

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)