4WL4 | pdb_00004wl4

Crystal structure of human carbonic anhydrase II in complex with the 6-hydroxy-chromene-2-thione inhibitor

PDB DOI: https://doi.org/10.2210/pdb4WL4/pdb

Classification: LYASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2014-10-06 Released: 2015-10-14
Deposition Author(s): Ferraroni, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.130 (Depositor), 0.131 (DCC)
R-Value Work:
0.109 (Depositor), 0.110 (DCC)
R-Value Observed:
0.110 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

New classes of carbonic anhydrase inhibitors

Ferraroni, M., Supuran, C.T., Carta, F., Bozdag, M., Scozzafava, A.

To be published.

Macromolecule Content

Total Structure Weight: 29.59 kDa
Atom Count: 2,552
Modeled Residue Count: 257
Deposited Residue Count: 260
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00918
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FC5 Query on FC5 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]	6-hydroxy-2H-chromene-2-thione C₉ H₆ O₂ S FGHZVFOCIYABBE-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]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
FC5	BindingDB: 4WL4	Ki: min: 2.00e+5, max: 2.85e+5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.130 (Depositor), 0.131 (DCC)
R-Value Work: 0.109 (Depositor), 0.110 (DCC)
R-Value Observed: 0.110 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.264	α = 90
b = 41.367	β = 104.21
c = 72.276	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.