5OGJ | pdb_00005ogj

Crystal structure of human carbonic anhydrase isozyme XIII with 2-(Cyclooctylamino)-3,5,6-trifluoro-4-[(2-hydroxyethyl)thio]benzenesulfonamide

PDB DOI: https://doi.org/10.2210/pdb5OGJ/pdb

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

Deposited: 2017-07-13 Released: 2018-08-01
Deposition Author(s): Manakova, E., Smirnov, A., Grazulis, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.06 Å
R-Value Free:
0.155 (Depositor), 0.156 (DCC)
R-Value Work:
0.132 (Depositor)
R-Value Observed:
0.134 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of human carbonic anhydrase isozyme XIII with 2-(Cyclooctylamino)-3,5,6-trifluoro-4-[(2-hydroxyethyl)thio]benzenesulfonamide

Smirnov, A., Manakova, E., Grazulis, S., Matulis, D.

To be published.

Macromolecule Content

Total Structure Weight: 61.49 kDa
Atom Count: 5,216
Modeled Residue Count: 522
Deposited Residue Count: 526
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8N1Q1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V90 Query on V90 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain R [auth A] MOL2 format, chain J [auth B] MOL2 format, chain R [auth A] mmCIF format, chain J [auth B] mmCIF format, chain R [auth A]	J [auth B], R [auth A]	2-(cyclooctylamino)-3,5,6-trifluoro-4-[(2-hydroxyethyl)sulfanyl]benzenesulfonamide C₁₆ H₂₃ F₃ N₂ O₃ S₂ ZUTOCUUMVDYVHW-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain R [auth A] Interactions & Density Focus chain J [auth B] Focus chain R [auth A]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain L [auth A] SDF format, chain O [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain L [auth A] MOL2 format, chain O [auth A] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain L [auth A] mmCIF format, chain O [auth A]	D [auth B], E [auth B], L [auth A], O [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain L [auth A] Focus chain O [auth A] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain L [auth A] Focus chain O [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain K [auth A] MOL2 format, chain C [auth B] MOL2 format, chain K [auth A] mmCIF format, chain C [auth B] mmCIF format, chain K [auth A]	C [auth B], K [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain K [auth A] Interactions & Density Focus chain C [auth B] Focus chain K [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A]	H [auth B], I [auth B], M [auth A], N [auth A], P [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth A] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain Q [auth A] MOL2 format, chain G [auth B] MOL2 format, chain Q [auth A] mmCIF format, chain G [auth B] mmCIF format, chain Q [auth A]	G [auth B], Q [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Focus chain Q [auth A] Interactions & Density Focus chain G [auth B] Focus chain Q [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
V90	BindingDB: 5OGJ	Kd: min: 1, max: 420 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.06 Å
R-Value Free: 0.155 (Depositor), 0.156 (DCC)
R-Value Work: 0.132 (Depositor)
R-Value Observed: 0.134 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.445	α = 90
b = 57.244	β = 90
c = 159.782	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

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Entry History

Deposition Data

Released Date: 2018-08-01

Deposition Author(s):

Manakova, E.

Smirnov, A.

Grazulis, S.

Revision History (Full details and data files)

Version 1.0: 2018-08-01
Type: Initial release
Version 1.1: 2024-01-17
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description