5LL9

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

PDB DOI: https://doi.org/10.2210/pdb5LL9/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: 1.45 Å
R-Value Free: 0.204
R-Value Work: 0.171
R-Value Observed: 0.174

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: 122.3 kDa
Atom Count: 9,959
Modelled Residue Count: 1,044
Deposited Residue Count: 1,052
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 12	A, B, C, D	263	Homo sapiens	Mutation(s): 0 Gene Names: CA12 EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for O43570 (Homo sapiens) Explore O43570 Go to UniProtKB: O43570
PHAROS: O43570 GTEx: ENSG00000074410
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43570
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 F [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D]	F [auth A], L [auth B], Q [auth C], V [auth D]	4-[2-(benzimidazol-1-yl)ethanoyl]-2-chloranyl-benzenesulfonamide C₁₅ H₁₂ Cl N₃ O₃ S SWJLGRBJIPSPCI-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain W [auth D] SDF format, chain R [auth C] MOL2 format, chain M [auth B] MOL2 format, chain W [auth D] MOL2 format, chain R [auth C] mmCIF format, chain M [auth B] mmCIF format, chain W [auth D] mmCIF format, chain R [auth C]	M [auth B], R [auth C], W [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain U [auth D]	E [auth A], K [auth B], P [auth C], U [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain U [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain S [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain S [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain S [auth C]	G [auth A] H [auth A] I [auth A] J [auth A] N [auth B] G [auth A], H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], S [auth C], T [auth C], X [auth D], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
6YQ	BindingDB: 5LL9	Kd: min: 8.4, max: 833 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.204
R-Value Work: 0.171
R-Value Observed: 0.174
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.298	α = 90
b = 73.887	β = 108.76
c = 91.285	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary