5PZS | pdb_00005pzs

Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(3-chlorophenyl)sulfonyl-3-[6-[(3-chlorophenyl)sulfonylcarbamoylamino]hexyl]urea

PDB DOI: https://doi.org/10.2210/pdb5PZS/pdb
Deposition Group: G_1002030 | Explore G_1002030

Classification: HYDROLASE/HYDROLASE inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-04-11 Released: 2019-01-09
Deposition Author(s): Ruf, A., Joseph, C., Alker, A., Banner, D., Tetaz, T., Benz, J., Kuhn, B., Rudolph, M.G., Yang, H., Shao, C., Burley, S.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free:
0.233 (Depositor), 0.233 (DCC)
R-Value Work:
0.174 (Depositor), 0.175 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(3-chlorophenyl)sulfonyl-3-[6-[(3-chlorophenyl)sulfonylcarbamoylamino]hexyl]urea

Ruf, A., Joseph, C., Alker, A., Banner, D., Tetaz, T., Benz, J., Kuhn, B., Rudolph, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 148.54 kDa
Atom Count: 10,417
Modeled Residue Count: 1,271
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, hCG_1640493 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
93Y Query on 93Y Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	N,N'-(hexane-1,6-diyldicarbamoyl)bis(3-chlorobenzene-1-sulfonamide) C₂₀ H₂₄ Cl₂ N₄ O₆ S₂ QXFHDZXCDGQHJF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
93Y	BindingDB: 5PZS	IC50: min: 8, max: 17 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.233 (Depositor), 0.233 (DCC)
R-Value Work: 0.174 (Depositor), 0.175 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.657	α = 90
b = 83.267	β = 90
c = 277.759	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-01-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-01-09
Type: Initial release
Version 1.1: 2019-01-16
Changes: Data collection
Version 1.2: 2019-02-06
Changes: Data collection, Database references, Structure summary
Version 1.3: 2021-02-10
Changes: Structure summary
Version 1.4: 2024-03-06
Changes: Advisory, Data collection, Database references, Refinement description