7CVN | pdb_00007cvn

The N-arylsulfonyl-indole-2-carboxamide-based inhibitors against fructose-1,6-bisphosphatase

PDB DOI: https://doi.org/10.2210/pdb7CVN/pdb

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

Deposited: 2020-08-26 Released: 2020-09-23
Deposition Author(s): Wang, X., Zhou, J., Xu, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.234 (Depositor), 0.232 (DCC)
R-Value Work:
0.163 (Depositor), 0.165 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Design,synthesis,biological evaluation and binding mode analysis of 7-nitro-indole-N-acylarylsulfonamide-based fructose-1,6-bisphosphatase inhibitors

Bie, J., Wang, X., Liu, S., Zhou, J., Liu, Q., Shen, Z., Xu, B.

(2020) Chinese Journal Of Medicinal Chemistry 30: 713-724

DOI: https://doi.org/10.14142/j.cnki.cn21-1313/r.2020.12.001

Macromolecule Content

Total Structure Weight: 150.94 kDa
Atom Count: 10,319
Modeled Residue Count: 1,280
Deposited Residue Count: 1,352
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-1,6-bisphosphatase 1	A, B, C, D	338	Homo sapiens	Mutation(s): 0 Gene Names: FBP1, FBP EC: 3.1.3.11
UniProt & NIH Common Fund Data Resources
Find proteins for P09467 (Homo sapiens) Explore P09467 Go to UniProtKB: P09467
PHAROS: P09467 GTEx: ENSG00000165140
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09467
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GJO (Subject of Investigation/LOI) Query on GJO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	4-(3-acetamidophenyl)-N-(4-methoxyphenyl)sulfonyl-7-nitro-1H-indole-2-carboxamide C₂₄ H₂₀ N₄ O₇ S NWBVAQWYAKYBIW-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
FBP (Subject of Investigation/LOI) Query on FBP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.234 (Depositor), 0.232 (DCC)
R-Value Work: 0.163 (Depositor), 0.165 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.57	α = 90
b = 83	β = 90
c = 278.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-09-23

Deposition Author(s):

Wang, X.

Zhou, J.

Xu, B.

Revision History (Full details and data files)

Version 1.0: 2020-09-23
Type: Initial release
Version 1.1: 2021-06-16
Changes: Database references, Structure summary
Version 1.2: 2023-11-29
Changes: Data collection, Database references, Refinement description

7CVN | pdb_00007cvn

The N-arylsulfonyl-indole-2-carboxamide-based inhibitors against fructose-1,6-bisphosphatase

Literature

Design,synthesis,biological evaluation and binding mode analysis of 7-nitro-indole-N-acylarylsulfonamide-based fructose-1,6-bisphosphatase inhibitors

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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