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Zinc in PDB 4k69: Crystal Structure of Human Chymase in Complex with Fragment Linked Benzimidazolone Inhibitor: (3S)-3-{3-[(6-Bromo-2-Oxo-2,3-Dihydro-1H- Indol-4-Yl)Methyl]-2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl}Hexanoic Acid

Enzymatic activity of Crystal Structure of Human Chymase in Complex with Fragment Linked Benzimidazolone Inhibitor: (3S)-3-{3-[(6-Bromo-2-Oxo-2,3-Dihydro-1H- Indol-4-Yl)Methyl]-2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl}Hexanoic Acid

All present enzymatic activity of Crystal Structure of Human Chymase in Complex with Fragment Linked Benzimidazolone Inhibitor: (3S)-3-{3-[(6-Bromo-2-Oxo-2,3-Dihydro-1H- Indol-4-Yl)Methyl]-2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl}Hexanoic Acid:
3.4.21.39;

Protein crystallography data

The structure of Crystal Structure of Human Chymase in Complex with Fragment Linked Benzimidazolone Inhibitor: (3S)-3-{3-[(6-Bromo-2-Oxo-2,3-Dihydro-1H- Indol-4-Yl)Methyl]-2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl}Hexanoic Acid, PDB code: 4k69 was solved by B.K.Collins, A.K.Padyana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.26 / 1.50
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 74.365, 74.365, 49.474, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.3

Other elements in 4k69:

The structure of Crystal Structure of Human Chymase in Complex with Fragment Linked Benzimidazolone Inhibitor: (3S)-3-{3-[(6-Bromo-2-Oxo-2,3-Dihydro-1H- Indol-4-Yl)Methyl]-2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl}Hexanoic Acid also contains other interesting chemical elements:

Bromine (Br) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Chymase in Complex with Fragment Linked Benzimidazolone Inhibitor: (3S)-3-{3-[(6-Bromo-2-Oxo-2,3-Dihydro-1H- Indol-4-Yl)Methyl]-2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl}Hexanoic Acid (pdb code 4k69). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human Chymase in Complex with Fragment Linked Benzimidazolone Inhibitor: (3S)-3-{3-[(6-Bromo-2-Oxo-2,3-Dihydro-1H- Indol-4-Yl)Methyl]-2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl}Hexanoic Acid, PDB code: 4k69:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4k69

Go back to Zinc Binding Sites List in 4k69
Zinc binding site 1 out of 2 in the Crystal Structure of Human Chymase in Complex with Fragment Linked Benzimidazolone Inhibitor: (3S)-3-{3-[(6-Bromo-2-Oxo-2,3-Dihydro-1H- Indol-4-Yl)Methyl]-2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl}Hexanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Chymase in Complex with Fragment Linked Benzimidazolone Inhibitor: (3S)-3-{3-[(6-Bromo-2-Oxo-2,3-Dihydro-1H- Indol-4-Yl)Methyl]-2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl}Hexanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:17.1
occ:1.00
 NE2 A:HIS25 2.1 12.4 1.0
OE1 A:GLU78 2.1 18.7 1.0
O A:HOH627 2.5 34.5 1.0
CD A:GLU78 2.9 18.7 1.0
OE2 A:GLU78 3.0 20.1 1.0
CE1 A:HIS25 3.1 15.0 1.0
CD2 A:HIS25 3.1 15.1 1.0
OG1 A:THR79A 4.0 12.4 1.0
CG2 A:THR79A 4.1 14.4 1.0
ND1 A:HIS25 4.2 14.5 1.0
CG A:HIS25 4.2 14.2 1.0
CG A:GLU78 4.3 16.4 1.0
O A:HOH614 4.5 21.4 1.0
CB A:THR79A 4.7 12.0 1.0
CB A:GLU78 4.8 17.7 1.0
CB A:PRO24 4.8 18.5 1.0

Zinc binding site 2 out of 2 in 4k69

Go back to Zinc Binding Sites List in 4k69
Zinc binding site 2 out of 2 in the Crystal Structure of Human Chymase in Complex with Fragment Linked Benzimidazolone Inhibitor: (3S)-3-{3-[(6-Bromo-2-Oxo-2,3-Dihydro-1H- Indol-4-Yl)Methyl]-2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl}Hexanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Chymase in Complex with Fragment Linked Benzimidazolone Inhibitor: (3S)-3-{3-[(6-Bromo-2-Oxo-2,3-Dihydro-1H- Indol-4-Yl)Methyl]-2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl}Hexanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:33.1
occ:1.00
 NE2 A:HIS233 2.4 26.9 1.0
O A:HOH593 2.6 38.0 1.0
CE1 A:HIS101 3.0 27.1 1.0
CD2 A:HIS233 3.2 22.8 1.0
ND1 A:HIS101 3.4 29.9 1.0
CE1 A:HIS233 3.4 23.3 1.0
O A:HOH448 3.6 31.0 1.0
NZ A:LYS93 3.9 40.1 1.0
NE2 A:HIS101 4.1 28.0 1.0
CD A:LYS93 4.2 29.3 1.0
CD2 A:LEU179 4.3 20.3 1.0
CG A:HIS233 4.4 23.6 1.0
CE1 A:TYR234 4.5 21.6 1.0
ND1 A:HIS233 4.5 24.1 1.0
CG A:HIS101 4.6 22.2 1.0
CE A:LYS93 4.6 37.4 1.0
OH A:TYR234 4.7 24.6 1.0
CE1 A:HIS91 4.7 19.7 1.0
CZ A:TYR234 4.8 20.3 1.0
NE2 A:HIS91 4.9 21.6 1.0
CD2 A:HIS101 4.9 26.1 1.0

Reference:

S.J.Taylor, A.K.Padyana, A.Abeywardane, S.Liang, M.H.Hao, S.De Lombaert, J.Proudfoot, B.S.Farmer, X.Li, B.Collins, L.Martin, D.R.Albaugh, M.Hill-Drzewi, S.S.Pullen, H.Takahashi. Discovery of Potent, Selective Chymase Inhibitors Via Fragment Linking Strategies. J.Med.Chem. V. 56 4465 2013.
ISSN: ISSN 0022-2623
PubMed: 23659209
DOI: 10.1021/JM400138Z
Page generated: Sun Oct 27 01:45:03 2024

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