5LLA

Crystal structure of human carbonic anhydrase isozyme XIII with 4-(1H-benzimidazol-1-ylacetyl)-2-chlorobenzenesulfonamide

PDB DOI: https://doi.org/10.2210/pdb5LLA/pdb

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

Deposited: 2016-07-27 Released: 2017-08-16
Deposition Author(s): Smirnov, A., Manakova, E., Grazulis, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.212
R-Value Work: 0.179
R-Value Observed: 0.182

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

Combinatorial Design of Isoform-Selective N-Alkylated Benzimidazole-Based Inhibitors of Carbonic Anhydrases

Capkauskaite, E., Linkuviene, V., Smirnov, A., Milinaviciute, G., Timm, D., Kasiliauskaite, A., Manakova, E., Grazulis, S., Matulis, D.

(2017) ChemistrySelect

DOI: https://doi.org/10.1002/slct.201700531

Macromolecule Content

Total Structure Weight: 60.57 kDa
Atom Count: 4,853
Modelled Residue Count: 516
Deposited Residue Count: 526
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 13	A [auth B], B [auth A]	263	Homo sapiens	Mutation(s): 0 Gene Names: CA13 EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N1Q1 (Homo sapiens) Explore Q8N1Q1 Go to UniProtKB: Q8N1Q1
PHAROS: Q8N1Q1 GTEx: ENSG00000185015
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N1Q1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6YQ Query on 6YQ Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain H [auth A] MOL2 format, chain D [auth B] MOL2 format, chain H [auth A] mmCIF format, chain D [auth B] mmCIF format, chain H [auth A]	D [auth B], H [auth A]	4-[2-(benzimidazol-1-yl)ethanoyl]-2-chloranyl-benzenesulfonamide C₁₅ H₁₂ Cl N₃ O₃ S SWJLGRBJIPSPCI-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain H [auth A] Interactions & Density Focus chain D [auth B] Focus chain H [auth A]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain I [auth A] MOL2 format, chain E [auth B] MOL2 format, chain I [auth A] mmCIF format, chain E [auth B] mmCIF format, chain I [auth A]	E [auth B], I [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain I [auth A] Interactions & Density Focus chain E [auth B] Focus chain I [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain G [auth A] MOL2 format, chain C [auth B] MOL2 format, chain G [auth A] mmCIF format, chain C [auth B] mmCIF format, chain G [auth A]	C [auth B], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain G [auth A] Interactions & Density Focus chain C [auth B] Focus chain G [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain J [auth A] MOL2 format, chain F [auth B] MOL2 format, chain J [auth A] mmCIF format, chain F [auth B] mmCIF format, chain J [auth A]	F [auth B], J [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain J [auth A] Interactions & Density Focus chain F [auth B] Focus chain J [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
6YQ	BindingDB: 5LLA	Kd: min: 0.19, max: 19 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.212
R-Value Work: 0.179
R-Value Observed: 0.182
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.023	α = 90
b = 57.276	β = 90
c = 159.284	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-08-16

Deposition Author(s):

Smirnov, A.

Manakova, E.

Grazulis, S.

Revision History (Full details and data files)

Version 1.0: 2017-08-16
Type: Initial release
Version 1.1: 2017-11-29
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5LLA

Crystal structure of human carbonic anhydrase isozyme XIII with 4-(1H-benzimidazol-1-ylacetyl)-2-chlorobenzenesulfonamide

Combinatorial Design of Isoform-Selective N-Alkylated Benzimidazole-Based Inhibitors of Carbonic Anhydrases

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)