4MDM

Nido-Carborane Carbonic Anhydrase Inhibitor

PDB DOI: https://doi.org/10.2210/pdb4MDM/pdb

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

Deposited: 2013-08-23 Released: 2014-01-01
Deposition Author(s): Brynda, J., Mader, P., Rezacova, P., Cigler, P., Gruner, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.201
R-Value Work: 0.167
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Carborane-based carbonic anhydrase inhibitors.

Brynda, J., Mader, P., Sicha, V., Fabry, M., Poncova, K., Bakardiev, M., Gruner, B., Cigler, P., Rezacova, P.

(2013) Angew Chem Int Ed Engl 52: 13760-13763

PubMed: 24307504 Search on PubMed
DOI: https://doi.org/10.1002/anie.201307583
Primary Citation of Related Structures:
4MDG, 4MDL, 4MDM

PubMed Abstract:
CA inhibitors: Human carbonic anhydrases (CAs) are diagnostic and therapeutic targets. Various carborane cages are shown to act as active-site-directed inhibitors, and substitution with a sulfamide group and other substituents leads to compounds with high selectivity towards the cancer-specific isozyme IX. Crystal structures of the carboranes in the active site provide information that can be applied to the structure-based design of specific inhibitors.

Organizational Affiliation

Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i. Vídeňská 1083, 142 20 Prague 4 (Czech Republic); Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nám. 2, 16610 Prague 6 (Czech Republic).

Macromolecule Content

Total Structure Weight: 29.37 kDa
Atom Count: 2,310
Modelled Residue Count: 258
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	258	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00918
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
26E Query on 26E 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]	7-(sulfamoylamino)methyl-7,8-dicarba-nido-undecaborane C₃ H₅ B₉ N₂ O₂ S VRKHBQSBPLXCRB-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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.201
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.01	α = 90
b = 41.3	β = 104.17
c = 72.06	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-01-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-01-01
Type: Initial release
Version 1.1: 2015-03-18
Changes: Structure summary
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations