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Chlorine in PDB 3qcm: Human Receptor Protein Tyrosine Phosphatase Gamma, Domain 1, in Complex with 2-[(3,4-Dichlorobenzyl)Sulfanyl]-4-{[3-({N-[2- (Methylamino)Ethyl]Glycyl}Amino)Phenyl]Ethynyl}Benzoic Acid

Enzymatic activity of Human Receptor Protein Tyrosine Phosphatase Gamma, Domain 1, in Complex with 2-[(3,4-Dichlorobenzyl)Sulfanyl]-4-{[3-({N-[2- (Methylamino)Ethyl]Glycyl}Amino)Phenyl]Ethynyl}Benzoic Acid

All present enzymatic activity of Human Receptor Protein Tyrosine Phosphatase Gamma, Domain 1, in Complex with 2-[(3,4-Dichlorobenzyl)Sulfanyl]-4-{[3-({N-[2- (Methylamino)Ethyl]Glycyl}Amino)Phenyl]Ethynyl}Benzoic Acid:
3.1.3.48;

Protein crystallography data

The structure of Human Receptor Protein Tyrosine Phosphatase Gamma, Domain 1, in Complex with 2-[(3,4-Dichlorobenzyl)Sulfanyl]-4-{[3-({N-[2- (Methylamino)Ethyl]Glycyl}Amino)Phenyl]Ethynyl}Benzoic Acid, PDB code: 3qcm was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.52 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.600, 74.600, 81.900, 90.00, 98.30, 90.00
R / Rfree (%) 20 / 24.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human Receptor Protein Tyrosine Phosphatase Gamma, Domain 1, in Complex with 2-[(3,4-Dichlorobenzyl)Sulfanyl]-4-{[3-({N-[2- (Methylamino)Ethyl]Glycyl}Amino)Phenyl]Ethynyl}Benzoic Acid (pdb code 3qcm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Human Receptor Protein Tyrosine Phosphatase Gamma, Domain 1, in Complex with 2-[(3,4-Dichlorobenzyl)Sulfanyl]-4-{[3-({N-[2- (Methylamino)Ethyl]Glycyl}Amino)Phenyl]Ethynyl}Benzoic Acid, PDB code: 3qcm:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3qcm

Go back to Chlorine Binding Sites List in 3qcm
Chlorine binding site 1 out of 4 in the Human Receptor Protein Tyrosine Phosphatase Gamma, Domain 1, in Complex with 2-[(3,4-Dichlorobenzyl)Sulfanyl]-4-{[3-({N-[2- (Methylamino)Ethyl]Glycyl}Amino)Phenyl]Ethynyl}Benzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Receptor Protein Tyrosine Phosphatase Gamma, Domain 1, in Complex with 2-[(3,4-Dichlorobenzyl)Sulfanyl]-4-{[3-({N-[2- (Methylamino)Ethyl]Glycyl}Amino)Phenyl]Ethynyl}Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2001

b:45.0
occ:1.00
CL35 A:NXW2001 0.0 45.0 1.0
C19 A:NXW2001 1.7 47.5 1.0
C20 A:NXW2001 2.7 49.4 1.0
C9 A:NXW2001 2.7 47.5 1.0
CL36 A:NXW2001 3.1 49.9 1.0
CD2 A:PHE1041 3.3 24.4 1.0
CG2 A:ILE950 3.5 27.9 1.0
CE2 A:PHE1041 3.5 26.0 1.0
CG1 A:VAL1038 3.9 29.8 1.0
C7 A:NXW2001 4.0 48.1 1.0
C12 A:NXW2001 4.0 47.8 1.0
CG A:TYR1023 4.1 28.7 1.0
CD1 A:TYR1023 4.1 29.5 1.0
CB A:TYR1023 4.2 26.4 1.0
CG1 A:ILE950 4.4 28.8 1.0
CG A:PHE1041 4.4 23.9 1.0
CD1 A:TYR1070 4.4 24.1 1.0
C16 A:NXW2001 4.5 46.7 1.0
CD1 A:ILE950 4.5 31.4 1.0
CB A:ILE950 4.5 28.5 1.0
CD2 A:TYR1023 4.6 29.5 1.0
CZ A:PHE1041 4.7 22.8 1.0
CE1 A:TYR1023 4.7 28.8 1.0
CB A:VAL1038 4.8 31.0 1.0
CG2 A:VAL1038 4.8 30.6 1.0
CG2 A:VAL1042 4.9 27.6 1.0
CB A:PHE1041 4.9 24.6 1.0

Chlorine binding site 2 out of 4 in 3qcm

Go back to Chlorine Binding Sites List in 3qcm
Chlorine binding site 2 out of 4 in the Human Receptor Protein Tyrosine Phosphatase Gamma, Domain 1, in Complex with 2-[(3,4-Dichlorobenzyl)Sulfanyl]-4-{[3-({N-[2- (Methylamino)Ethyl]Glycyl}Amino)Phenyl]Ethynyl}Benzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Receptor Protein Tyrosine Phosphatase Gamma, Domain 1, in Complex with 2-[(3,4-Dichlorobenzyl)Sulfanyl]-4-{[3-({N-[2- (Methylamino)Ethyl]Glycyl}Amino)Phenyl]Ethynyl}Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2001

b:49.9
occ:1.00
CL36 A:NXW2001 0.0 49.9 1.0
C20 A:NXW2001 1.7 49.4 1.0
C12 A:NXW2001 2.7 47.8 1.0
C19 A:NXW2001 2.7 47.5 1.0
CL35 A:NXW2001 3.1 45.0 1.0
N A:TYR1070 3.4 24.7 1.0
CA A:TYR1070 3.5 22.9 1.0
CB A:TYR1070 3.7 23.2 1.0
CG2 A:THR1069 3.8 25.8 1.0
O A:ARG1066 3.8 31.1 1.0
C A:THR1069 3.9 29.7 1.0
C16 A:NXW2001 3.9 46.7 1.0
CG1 A:VAL1038 4.0 29.8 1.0
C9 A:NXW2001 4.0 47.5 1.0
CB A:THR1069 4.2 31.2 1.0
CD1 A:ILE1073 4.3 27.2 1.0
O A:THR1069 4.4 31.4 1.0
CD1 A:TYR1070 4.4 24.1 1.0
C7 A:NXW2001 4.5 48.1 1.0
CG A:TYR1070 4.6 22.8 1.0
CG2 A:ILE950 4.6 27.9 1.0
CA A:THR1069 4.6 25.7 1.0
CD1 A:ILE950 4.7 31.4 1.0
CG2 A:VAL1042 4.7 27.6 1.0
C A:ARG1066 4.9 30.8 1.0
CE2 A:PHE1111 4.9 42.3 1.0
C A:TYR1070 4.9 27.9 1.0

Chlorine binding site 3 out of 4 in 3qcm

Go back to Chlorine Binding Sites List in 3qcm
Chlorine binding site 3 out of 4 in the Human Receptor Protein Tyrosine Phosphatase Gamma, Domain 1, in Complex with 2-[(3,4-Dichlorobenzyl)Sulfanyl]-4-{[3-({N-[2- (Methylamino)Ethyl]Glycyl}Amino)Phenyl]Ethynyl}Benzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Receptor Protein Tyrosine Phosphatase Gamma, Domain 1, in Complex with 2-[(3,4-Dichlorobenzyl)Sulfanyl]-4-{[3-({N-[2- (Methylamino)Ethyl]Glycyl}Amino)Phenyl]Ethynyl}Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2001

b:54.8
occ:1.00
CL35 B:NXW2001 0.0 54.8 1.0
C19 B:NXW2001 1.7 54.0 1.0
C20 B:NXW2001 2.7 50.9 1.0
C9 B:NXW2001 2.7 53.0 1.0
CL36 B:NXW2001 3.1 46.0 1.0
CD2 B:PHE1041 3.3 39.6 1.0
CG2 B:ILE950 3.5 38.6 1.0
CE2 B:PHE1041 3.5 42.1 1.0
CG1 B:VAL1038 3.9 44.5 1.0
C12 B:NXW2001 4.0 51.4 1.0
C7 B:NXW2001 4.0 52.1 1.0
CG B:TYR1023 4.1 38.9 1.0
CD1 B:TYR1023 4.1 40.6 1.0
CB B:TYR1023 4.2 38.7 1.0
CG1 B:ILE950 4.4 38.4 1.0
CG B:PHE1041 4.4 38.1 1.0
CD2 B:TYR1070 4.4 28.9 1.0
CD1 B:ILE950 4.5 45.1 1.0
CB B:ILE950 4.5 39.3 1.0
C16 B:NXW2001 4.5 52.4 1.0
CZ B:PHE1041 4.7 40.7 1.0
CD2 B:TYR1023 4.7 39.2 1.0
CE1 B:TYR1023 4.7 40.4 1.0
CB B:VAL1038 4.7 44.8 1.0
CG2 B:VAL1038 4.8 44.4 1.0
CG2 B:VAL1042 4.9 32.8 1.0
CB B:PHE1041 4.9 36.5 1.0
CA B:VAL1038 5.0 41.4 1.0

Chlorine binding site 4 out of 4 in 3qcm

Go back to Chlorine Binding Sites List in 3qcm
Chlorine binding site 4 out of 4 in the Human Receptor Protein Tyrosine Phosphatase Gamma, Domain 1, in Complex with 2-[(3,4-Dichlorobenzyl)Sulfanyl]-4-{[3-({N-[2- (Methylamino)Ethyl]Glycyl}Amino)Phenyl]Ethynyl}Benzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human Receptor Protein Tyrosine Phosphatase Gamma, Domain 1, in Complex with 2-[(3,4-Dichlorobenzyl)Sulfanyl]-4-{[3-({N-[2- (Methylamino)Ethyl]Glycyl}Amino)Phenyl]Ethynyl}Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2001

b:46.0
occ:1.00
CL36 B:NXW2001 0.0 46.0 1.0
C20 B:NXW2001 1.7 50.9 1.0
C12 B:NXW2001 2.7 51.4 1.0
C19 B:NXW2001 2.7 54.0 1.0
CL35 B:NXW2001 3.1 54.8 1.0
N B:TYR1070 3.4 25.2 1.0
CA B:TYR1070 3.5 24.6 1.0
CB B:TYR1070 3.7 25.2 1.0
CG2 B:THR1069 3.8 27.9 1.0
O B:ARG1066 3.8 35.2 1.0
C B:THR1069 3.9 28.5 1.0
CG1 B:VAL1038 4.0 44.5 1.0
C16 B:NXW2001 4.0 52.4 1.0
C9 B:NXW2001 4.0 53.0 1.0
CB B:THR1069 4.1 30.1 1.0
CD1 B:ILE1073 4.3 34.5 1.0
O B:THR1069 4.4 28.5 1.0
CD2 B:TYR1070 4.4 28.9 1.0
C7 B:NXW2001 4.5 52.1 1.0
CG B:TYR1070 4.6 28.2 1.0
CG2 B:ILE950 4.6 38.6 1.0
CA B:THR1069 4.6 25.3 1.0
CD1 B:ILE950 4.7 45.1 1.0
CG2 B:VAL1042 4.7 32.8 1.0
C B:ARG1066 4.9 34.6 1.0
CE2 B:PHE1111 4.9 44.9 1.0
C B:TYR1070 4.9 29.1 1.0

Reference:

S.Sheriff, B.R.Beno, W.Zhai, W.A.Kostich, P.A.Mcdonnell, K.Kish, V.Goldfarb, M.Gao, S.E.Kiefer, J.Yanchunas, Y.Huang, S.Shi, S.Zhu, C.Dzierba, J.Bronson, J.E.Macor, K.K.Appiah, R.S.Westphal, J.O'connell, S.W.Gerritz. Small Molecule Receptor Protein Tyrosine Phosphatase [Gamma](Rptp[Gamma]) Ligands That Inhibit Phosphatase Activity Via Perturbation of the Tryptophan-Proline-Aspartate (Wpd) Loop J.Med.Chem. V. 54 6548 2011.
ISSN: ISSN 0022-2623
PubMed: 21882820
DOI: 10.1021/JM2003766
Page generated: Fri Jul 11 09:22:43 2025

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