Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.55 kDa 
• Atom Count: 2256 
• Residue Count: 256 
• Unique protein chains: 1

1CIL

THE POSITIONS OF HIS-64 AND A BOUND WATER IN HUMAN CARBONIC ANHYDRASE II UPON BINDING THREE STRUCTURALLY RELATED INHIBITORS

• DOI: 10.2210/pdb1CIL/pdb

• Classification: LYASE(OXO-ACID)
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1993-10-20 Released: 1994-01-31 
• Deposition Author(s): Smith, G.M., Alexander, R.S., Christianson, D.W., Mckeever, B.M., Ponticello, G.S., Springer, J.P., Randall, W.C., Baldwin, J.J., Habecker, C.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å

Literature

Positions of His-64 and a bound water in human carbonic anhydrase II upon binding three structurally related inhibitors.

Smith, G.M., Alexander, R.S., Christianson, D.W., McKeever, B.M., Ponticello, G.S., Springer, J.P., Randall, W.C., Baldwin, J.J., Habecker, C.N.

(1994) Protein Sci 3: 118-125

• PubMed: 8142888 
• DOI: 10.1002/pro.5560030115
• Primary Citation of Related Structures:  
  1CIN, 1CIM, 1CIL


• PubMed Abstract: 
  

The 3-dimensional structure of human carbonic anhydrase II (HCAII; EC 4.2.1.1) complexed with 3 structurally related inhibitors, 1a, 1b, and 1c, has been determined by X-ray crystallographic methods. The 3 inhibitors (1a = C8H12N2O4S3) vary only in the length of the substituent on the 4-amino group: 1a, proton; 1b, methyl; and 1c, ethyl. The binding constants (Ki's) for 1a, 1b, and 1c to HCAII are 1.52, 1.88, and 0.37 nM, respectively. These structures were solved to learn if any structural cause could be found for the difference in binding. In the complex with inhibitors 1a and 1b, electron density can be observed for His-64 and a bound water molecule in the native positions. When inhibitor 1c is bound, the side chain attached to the 4-amino group is positioned so that His-64 can only occupy the alternate position and the bound water is absent. While a variety of factors contribute to the observed binding constants, the major reason 1c binds tighter to HCAII than does 1a or 1b appears to be entropy: the increase in entropy when the bound water molecule is released contributes to the increase in binding and overcomes the small penalty for putting the His-64 side chain in a higher energy state.

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Organizational Affiliation: 

Merck Research Laboratories, West Point, Pennsylvania 19486.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBONIC ANHYDRASE II	A	259	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
NIH Common Fund Data Resources
PHAROS  P00918 GTEx  ENSG00000104267

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ETS	A	(4S-TRANS)-4-(ETHYLAMINO)-5,6-DIHYDRO-6-METHYL-4H-THIENO(2,3-B)THIOPYRAN-2-SULFONAMIDE-7,7-DIOXIDE C10 H16 N2 O4 S3 IAVUPMFITXYVAF-XPUUQOCRSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ETS	Ki:  0.3720000088214874   nM  Binding MOAD
ETS	Ki:  0.2800000011920929   nM  BindingDB
ETS	IC50:  43   nM  BindingDB
ETS	IC50:  3.740000009536743   nM  BindingDB
ETS	Ki:  0.20000000298023224   nM  BindingDB
ETS	Ki:  9.100000381469727   nM  BindingDB
ETS	Ki:  25   nM  BindingDB
ETS	Ki :  0.3700000047683716   nM  PDBBind
ETS	IC50:  7.099999904632568   nM  BindingDB
ETS	Ki:  2   nM  BindingDB
ETS	Kd:  0.03999999910593033   nM  BindingDB
ETS	Ki:  9   nM  BindingDB
ETS	Ki:  25.020000457763672   nM  BindingDB
ETS	Ki:  0.5099999904632568   nM  BindingDB
ETS	IC50:  26.610000610351562   nM  BindingDB
ETS	IC50:  0.18000000715255737   nM  BindingDB
ETS	Ki:  0.3700000047683716   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.87	α = 90
b = 42.13	β = 104.55
c = 72.92	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1993-10-20 
• Released Date: 1994-01-31 
Deposition Author(s): Smith, G.M., Alexander, R.S., Christianson, D.W., Mckeever, B.M., Ponticello, G.S., Springer, J.P., Randall, W.C., Baldwin, J.J., Habecker, C.N.

Revision History 

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance