6ZR8

The crystal structure of 2-(4-Benzhydrylpiperazin-1-yl)-N-(4-sulfamoylphenyl)acetamide in complex with human carbonic anhydrase II

PDB DOI: https://doi.org/10.2210/pdb6ZR8/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-07-11 Released: 2021-06-16
Deposition Author(s): Di Fiore, A., De Simone, G., D'Ambrosio, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.199
R-Value Work: 0.164

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

The crystal structures of 2-(4-benzhydrylpiperazin-1-yl)-N-(4-sulfamoylphenyl)acetamide in complex with human carbonic anhydrase II and VII provide insights into selective CA inhibitor development

D'Ambrosio, K., Di Fiore, A., Buonanno, M., Kumari, S., Tiwari, M., Supuran, C.T., Mishra, C.B., Monti, S.M., De Simone, G.

(2021) New J Chem 45: 147-152

DOI: https://doi.org/10.1039/D0NJ03544K

Macromolecule Content

Total Structure Weight: 30.01 kDa
Atom Count: 2,332
Modelled Residue Count: 260
Deposited Residue Count: 262
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	262	Homo sapiens	Mutation(s): 0 Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918 Go to UniProtKB: P00918
PHAROS: P00918 GTEx: ENSG00000104267
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00918
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QOZ (Subject of Investigation/LOI) Query on QOZ Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-[4-(diphenylmethyl)piperazin-1-yl]-~{N}-(4-sulfamoylphenyl)ethanamide C₂₅ H₂₈ N₄ O₃ S MZCJQCUNQFZSCL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
QOZ	BindingDB: 6ZR8	Ki: 43 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.199
R-Value Work: 0.164
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.26	α = 90
b = 41.33	β = 104.26
c = 71.64	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-06-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-06-16
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.