6SDJ | pdb_00006sdj

Human Carbonic Anhydrase II in complex with (R)-1-aminopropan-2-ol

• PDB DOI: https://doi.org/10.2210/pdb6SDJ/pdb

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


• Deposited: 2019-07-27 Released: 2020-04-15 
• Deposition Author(s): Gloeckner, S., Heine, A., Klebe, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free: 
  0.140 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.128 (Depositor), 0.128 (DCC) 
• R-Value Observed: 
  0.129 (Depositor) 

Starting Model: experimental

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 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.

---

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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.06 kDa 
• Atom Count: 2,579 
• Modeled Residue Count: 258 
• 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 (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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BE7	F [auth A], G [auth A]	(4-CARBOXYPHENYL)(CHLORO)MERCURY C7 H5 Cl Hg O2 YFZOUMNUDGGHIW-UHFFFAOYSA-M
HG	D [auth A], E [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
J3K (Subject of Investigation/LOI)	C [auth A]	(2~{R})-1-azanylpropan-2-ol C3 H9 N O HXKKHQJGJAFBHI-GSVOUGTGSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free:  0.140 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.128 (Depositor), 0.128 (DCC) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.359	α = 90
b = 41.103	β = 104.187
c = 72.174	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: 2020-04-15 
Deposition Author(s): Gloeckner, S., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2020-04-15
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-01-24
  Changes: Refinement description