8S4F

Human carbonic anhydrase I covalently bound to AV21-08

PDB DOI: https://doi.org/10.2210/pdb8S4F/pdb

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

Deposited: 2024-02-21 Released: 2024-12-18
Deposition Author(s): Manakova, E.N., Grazulis, S., Paketuryte-Latve, V., Vaskevicius, A., Smirnov, A.
Funding Organization(s): iNEXT-Discovery

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.234
R-Value Work: 0.202
R-Value Observed: 0.205

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Targeted anticancer pre-vinylsulfone covalent inhibitors of carbonic anhydrase IX

Vaskevicius, A., Baronas, D., Leitans, J., Kvietkauskaite, A., Ruksenaite, A., Manakova, E., Toleikis, Z., Kaupinis, A., Kazaks, A., Gedgaudas, M., Mickeviciute, A., Juozapaitiene, V., Schioth, H.B., Jaudzems, K., Valius, M., Tars, K., Grazulis, S., Meyer-Almes, F.J., Matuliene, J., Zubriene, A., Dudutiene, V., Matulis, D.

(2024) Elife

DOI: https://doi.org/10.7554/elife.101401.2

Macromolecule Content

Total Structure Weight: 59.3 kDa
Atom Count: 4,702
Modelled Residue Count: 513
Deposited Residue Count: 520
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 1	A, B	260	Homo sapiens	Mutation(s): 0 Gene Names: CA1 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P00915 (Homo sapiens) Explore P00915 Go to UniProtKB: P00915
PHAROS: P00915 GTEx: ENSG00000133742
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00915
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VV8 (Subject of Investigation/LOI) Query on VV8 Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A]	J [auth A], N [auth B]	3-(cyclooctylamino)-4-ethylsulfonyl-2,5,6-tris(fluoranyl)benzenesulfonamide C₁₆ H₂₃ F₃ N₂ O₄ S₂ JATZJQNOFRECGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Interactions & Density Focus chain J [auth A] Focus chain N [auth B]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PPI Query on PPI 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]	PROPANOIC ACID C₃ H₆ O₂ XBDQKXXYIPTUBI-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain K [auth B]	C [auth A], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	G [auth A], H [auth A], I [auth A], L [auth B], M [auth B]	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 L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]