5M78

Human Carbonic Anhydrase II in complex with fragment-like inhibitor.

• PDB DOI: https://doi.org/10.2210/pdb5M78/pdb

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


• Deposited: 2016-10-27 Released: 2017-12-20 
• Deposition Author(s): Gloeckner, S., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.144 
• R-Value Work: 0.125 
• R-Value Observed: 0.126 

Literature

A Proof-of-Concept Fragment Screening of a Hit-Validated 96-Compounds Library against Human Carbonic Anhydrase II.

Glockner, S., Heine, A., Klebe, G.

(2020) Biomolecules 10

• PubMed: 32235320 
• DOI: https://doi.org/10.3390/biom10040518
• Primary Citation of Related Structures:  
  5M78, 6RM1, 6RMP, 6S9Z, 6SAC, 6SAS, 6SAY, 6SB7, 6SDJ


• PubMed Abstract: 
  

  Fragment screening is a powerful tool to identify and characterize binding pockets in proteins. We herein present the results of a proof-of-concept screening campaign of a versatile 96-entry fragment library from our laboratory against the drug target and model protein human carbonic anhydrase II. The screening revealed a novel chemotype for carbonic anhydrase inhibition, as well as less common non-covalent interaction types and unexpected covalent linkages. Lastly, different runs of the PanDDA tool reveal a practical hint for its application.

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Organizational Affiliation: 

Institute for Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.41 kDa 
• Atom Count: 2,499 
• Modelled Residue Count: 259 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	265	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MBO	D [auth A]	MERCURIBENZOIC ACID C7 H5 Hg O2 FVFZSVRSDNUCGG-UHFFFAOYSA-N
SAL	E [auth A]	2-HYDROXYBENZOIC ACID C7 H6 O3 YGSDEFSMJLZEOE-UHFFFAOYSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SAL	BindingDB:  5M78	Ki: min: 7100, max: 7.40e+5 (nM) from 3 assay(s)
		IC50: 6.80e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.144 
• R-Value Work: 0.125 
• R-Value Observed: 0.126 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.439	α = 90
b = 41.423	β = 104.75
c = 72.243	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Gloeckner, S., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2020-04-15
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description