2FOY | pdb_00002foy

Human Carbonic Anhydrase I complexed with a two-prong inhibitor

PDB DOI: https://doi.org/10.2210/pdb2FOY/pdb

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

Deposited: 2006-01-14 Released: 2006-04-04
Deposition Author(s): Jude, K.M., Banerjee, A.L., Haldar, M.K., Manokaran, S., Roy, B., Mallik, S., Srivastava, D.K., Christianson, D.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.243 (Depositor), 0.236 (DCC)
R-Value Work:
0.220 (Depositor), 0.211 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Ultrahigh resolution crystal structures of human carbonic anhydrases I and II complexed with two-prong inhibitors reveal the molecular basis of high affinity.

Jude, K.M., Banerjee, A.L., Haldar, M.K., Manokaran, S., Roy, B., Mallik, S., Srivastava, D.K., Christianson, D.W.

(2006) J Am Chem Soc 128: 3011-3018

PubMed: 16506782 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/ja057257n
Primary Citation Related Structures:
2FOQ, 2FOS, 2FOU, 2FOV, 2FOY

PubMed Abstract:
The atomic-resolution crystal structures of human carbonic anhydrases I and II complexed with "two-prong" inhibitors are reported. Each inhibitor contains a benzenesulfonamide prong and a cupric iminodiacetate (IDA-Cu(2+)) prong separated by linkers of different lengths and compositions. The ionized NH(-) group of each benzenesulfonamide coordinates to the active site Zn(2+) ion; the IDA-Cu(2+) prong of the tightest-binding inhibitor, BR30, binds to H64 of CAII and H200 of CAI. This work provides the first evidence verifying the structural basis of nanomolar affinity measured for two-prong inhibitors targeting the carbonic anhydrases.

Organizational Affiliation

Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.

Macromolecule Content

Total Structure Weight: 60.21 kDa
Atom Count: 4,750
Modeled Residue Count: 513
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

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| 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 (UniProt)
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00915
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B30 Query on B30 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	{2,2'-[(2-{[4-(AMINOSULFONYL)BENZOYL]AMINO}ETHYL)IMINO]DIACETATO(2-)-KAPPAO}COPPER C₁₃ H₁₅ Cu N₃ O₇ S IZSCVVCMRVDVFM-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.243 (Depositor), 0.236 (DCC)
R-Value Work: 0.220 (Depositor), 0.211 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.219	α = 90
b = 72.608	β = 90
c = 121.949	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-04-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-04-04
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description