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Chlorine in PDB 4jh0: Crystal Structure of Dipeptidyl-Peptidase 4 (CD26, Adenosine Deaminase Complexing Protein 2) (Dpp-IV-Wt) Complex with Bms-767778 Aka 2-(3- (Aminomethyl)-4-(2,4- Dichlorophenyl)-2-Methyl-5-Oxo-5,7-Dihydro-6H- Pyrrolo[3,4- B]Pyridin-6-Yl)-N,N-Dimethylacetamide

Enzymatic activity of Crystal Structure of Dipeptidyl-Peptidase 4 (CD26, Adenosine Deaminase Complexing Protein 2) (Dpp-IV-Wt) Complex with Bms-767778 Aka 2-(3- (Aminomethyl)-4-(2,4- Dichlorophenyl)-2-Methyl-5-Oxo-5,7-Dihydro-6H- Pyrrolo[3,4- B]Pyridin-6-Yl)-N,N-Dimethylacetamide

All present enzymatic activity of Crystal Structure of Dipeptidyl-Peptidase 4 (CD26, Adenosine Deaminase Complexing Protein 2) (Dpp-IV-Wt) Complex with Bms-767778 Aka 2-(3- (Aminomethyl)-4-(2,4- Dichlorophenyl)-2-Methyl-5-Oxo-5,7-Dihydro-6H- Pyrrolo[3,4- B]Pyridin-6-Yl)-N,N-Dimethylacetamide:
3.4.14.5;

Protein crystallography data

The structure of Crystal Structure of Dipeptidyl-Peptidase 4 (CD26, Adenosine Deaminase Complexing Protein 2) (Dpp-IV-Wt) Complex with Bms-767778 Aka 2-(3- (Aminomethyl)-4-(2,4- Dichlorophenyl)-2-Methyl-5-Oxo-5,7-Dihydro-6H- Pyrrolo[3,4- B]Pyridin-6-Yl)-N,N-Dimethylacetamide, PDB code: 4jh0 was solved by H.E.Klei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.95 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.311, 67.105, 423.771, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 27.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Dipeptidyl-Peptidase 4 (CD26, Adenosine Deaminase Complexing Protein 2) (Dpp-IV-Wt) Complex with Bms-767778 Aka 2-(3- (Aminomethyl)-4-(2,4- Dichlorophenyl)-2-Methyl-5-Oxo-5,7-Dihydro-6H- Pyrrolo[3,4- B]Pyridin-6-Yl)-N,N-Dimethylacetamide (pdb code 4jh0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Dipeptidyl-Peptidase 4 (CD26, Adenosine Deaminase Complexing Protein 2) (Dpp-IV-Wt) Complex with Bms-767778 Aka 2-(3- (Aminomethyl)-4-(2,4- Dichlorophenyl)-2-Methyl-5-Oxo-5,7-Dihydro-6H- Pyrrolo[3,4- B]Pyridin-6-Yl)-N,N-Dimethylacetamide, PDB code: 4jh0:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4jh0

Go back to Chlorine Binding Sites List in 4jh0
Chlorine binding site 1 out of 4 in the Crystal Structure of Dipeptidyl-Peptidase 4 (CD26, Adenosine Deaminase Complexing Protein 2) (Dpp-IV-Wt) Complex with Bms-767778 Aka 2-(3- (Aminomethyl)-4-(2,4- Dichlorophenyl)-2-Methyl-5-Oxo-5,7-Dihydro-6H- Pyrrolo[3,4- B]Pyridin-6-Yl)-N,N-Dimethylacetamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Dipeptidyl-Peptidase 4 (CD26, Adenosine Deaminase Complexing Protein 2) (Dpp-IV-Wt) Complex with Bms-767778 Aka 2-(3- (Aminomethyl)-4-(2,4- Dichlorophenyl)-2-Methyl-5-Oxo-5,7-Dihydro-6H- Pyrrolo[3,4- B]Pyridin-6-Yl)-N,N-Dimethylacetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl801

b:21.9
occ:1.00
 CL1 A:1MD801 0.0 21.9 1.0
C21 A:1MD801 1.7 21.9 1.0
C20 A:1MD801 2.6 21.9 1.0
C14 A:1MD801 2.7 21.9 1.0
C1 A:1MD801 3.0 21.9 1.0
ND2 A:ASN710 3.1 20.8 1.0
OH A:TYR662 3.3 27.8 1.0
C4 A:1MD801 3.5 21.9 1.0
NH2 A:ARG125 3.6 25.3 1.0
CG A:ASN710 3.7 20.0 1.0
C2 A:1MD801 3.7 21.9 1.0
N16 A:1MD801 3.7 21.9 1.0
OD1 A:ASN710 3.8 21.1 1.0
OE2 A:GLU205 3.8 18.4 1.0
NE2 A:HIS740 3.8 21.1 1.0
C9 A:1MD801 3.9 21.9 1.0
OG A:SER630 3.9 36.1 1.0
C19 A:1MD801 3.9 21.9 1.0
O1 A:1MD801 3.9 21.9 1.0
C17 A:1MD801 4.0 21.9 1.0
CD2 A:HIS740 4.0 25.8 1.0
C15 A:1MD801 4.3 21.9 1.0
C6 A:1MD801 4.4 21.9 1.0
CZ A:TYR662 4.4 29.4 1.0
C18 A:1MD801 4.5 21.9 1.0
CE1 A:HIS740 4.5 22.5 1.0
C3 A:1MD801 4.6 21.9 1.0
CG A:HIS740 4.8 24.5 1.0
CB A:ASN710 4.8 21.6 1.0
N1 A:1MD801 4.8 21.9 1.0
CE1 A:TYR662 4.9 27.9 1.0
N4 A:1MD801 4.9 21.9 1.0
CZ A:ARG125 4.9 29.8 1.0
CD A:GLU205 5.0 24.6 1.0
CB A:SER630 5.0 31.3 1.0

Chlorine binding site 2 out of 4 in 4jh0

Go back to Chlorine Binding Sites List in 4jh0
Chlorine binding site 2 out of 4 in the Crystal Structure of Dipeptidyl-Peptidase 4 (CD26, Adenosine Deaminase Complexing Protein 2) (Dpp-IV-Wt) Complex with Bms-767778 Aka 2-(3- (Aminomethyl)-4-(2,4- Dichlorophenyl)-2-Methyl-5-Oxo-5,7-Dihydro-6H- Pyrrolo[3,4- B]Pyridin-6-Yl)-N,N-Dimethylacetamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Dipeptidyl-Peptidase 4 (CD26, Adenosine Deaminase Complexing Protein 2) (Dpp-IV-Wt) Complex with Bms-767778 Aka 2-(3- (Aminomethyl)-4-(2,4- Dichlorophenyl)-2-Methyl-5-Oxo-5,7-Dihydro-6H- Pyrrolo[3,4- B]Pyridin-6-Yl)-N,N-Dimethylacetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl801

b:21.9
occ:1.00
 CL2 A:1MD801 0.0 21.9 1.0
C19 A:1MD801 1.7 21.9 1.0
C20 A:1MD801 2.7 21.9 1.0
C18 A:1MD801 2.7 21.9 1.0
CG2 A:VAL656 3.1 26.4 1.0
CD2 A:TYR631 4.0 23.8 1.0
C21 A:1MD801 4.0 21.9 1.0
OG A:SER630 4.0 36.1 1.0
CH2 A:TRP659 4.0 22.2 1.0
N A:TYR631 4.0 27.6 1.0
C17 A:1MD801 4.1 21.9 1.0
CZ3 A:TRP659 4.1 19.2 1.0
CA A:TYR631 4.1 26.3 1.0
CB A:TYR631 4.2 23.9 1.0
CE2 A:TYR662 4.2 28.5 1.0
CZ A:TYR662 4.3 29.4 1.0
CD2 A:TYR662 4.4 27.9 1.0
CB A:VAL656 4.4 26.9 1.0
CG2 A:VAL711 4.5 20.9 1.0
CE1 A:TYR662 4.5 27.9 1.0
CG A:TYR631 4.5 23.9 1.0
C14 A:1MD801 4.6 21.9 1.0
C A:SER630 4.6 29.9 1.0
CE1 A:TYR666 4.6 35.8 1.0
CG A:TYR662 4.6 30.4 1.0
CD1 A:TYR662 4.7 27.9 1.0
OH A:TYR662 4.7 27.8 1.0
OH A:TYR666 4.9 33.6 1.0
CZ A:TYR666 4.9 34.3 1.0
CE2 A:TYR631 5.0 24.9 1.0

Chlorine binding site 3 out of 4 in 4jh0

Go back to Chlorine Binding Sites List in 4jh0
Chlorine binding site 3 out of 4 in the Crystal Structure of Dipeptidyl-Peptidase 4 (CD26, Adenosine Deaminase Complexing Protein 2) (Dpp-IV-Wt) Complex with Bms-767778 Aka 2-(3- (Aminomethyl)-4-(2,4- Dichlorophenyl)-2-Methyl-5-Oxo-5,7-Dihydro-6H- Pyrrolo[3,4- B]Pyridin-6-Yl)-N,N-Dimethylacetamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Dipeptidyl-Peptidase 4 (CD26, Adenosine Deaminase Complexing Protein 2) (Dpp-IV-Wt) Complex with Bms-767778 Aka 2-(3- (Aminomethyl)-4-(2,4- Dichlorophenyl)-2-Methyl-5-Oxo-5,7-Dihydro-6H- Pyrrolo[3,4- B]Pyridin-6-Yl)-N,N-Dimethylacetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl801

b:21.9
occ:1.00
 CL1 B:1MD801 0.0 21.9 1.0
C21 B:1MD801 1.7 21.9 1.0
C20 B:1MD801 2.6 21.9 1.0
C14 B:1MD801 2.7 21.9 1.0
C1 B:1MD801 3.1 21.9 1.0
OH B:TYR662 3.4 42.1 1.0
C4 B:1MD801 3.5 21.9 1.0
NH2 B:ARG125 3.6 28.7 1.0
N16 B:1MD801 3.6 21.9 1.0
O1 B:1MD801 3.6 21.9 1.0
ND2 B:ASN710 3.7 24.8 1.0
NE2 B:HIS740 3.7 25.4 1.0
OD1 B:ASN710 3.8 20.3 1.0
C2 B:1MD801 3.8 21.9 1.0
C9 B:1MD801 3.8 21.9 1.0
OE2 B:GLU205 3.9 28.1 1.0
C19 B:1MD801 3.9 21.9 1.0
OG B:SER630 4.0 29.6 1.0
CG B:ASN710 4.0 27.3 1.0
CD2 B:HIS740 4.0 21.4 1.0
C17 B:1MD801 4.0 21.9 1.0
C15 B:1MD801 4.3 21.9 1.0
C6 B:1MD801 4.4 21.9 1.0
CE1 B:HIS740 4.4 26.3 1.0
O B:HOH903 4.5 44.1 1.0
C18 B:1MD801 4.5 21.9 1.0
CZ B:TYR662 4.5 45.6 1.0
C3 B:1MD801 4.6 21.9 1.0
CZ B:ARG125 4.8 33.0 1.0
CG B:HIS740 4.8 24.0 1.0
N1 B:1MD801 4.9 21.9 1.0
CG2 B:VAL711 4.9 22.1 1.0
CB B:SER630 5.0 29.1 1.0
N4 B:1MD801 5.0 21.9 1.0

Chlorine binding site 4 out of 4 in 4jh0

Go back to Chlorine Binding Sites List in 4jh0
Chlorine binding site 4 out of 4 in the Crystal Structure of Dipeptidyl-Peptidase 4 (CD26, Adenosine Deaminase Complexing Protein 2) (Dpp-IV-Wt) Complex with Bms-767778 Aka 2-(3- (Aminomethyl)-4-(2,4- Dichlorophenyl)-2-Methyl-5-Oxo-5,7-Dihydro-6H- Pyrrolo[3,4- B]Pyridin-6-Yl)-N,N-Dimethylacetamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Dipeptidyl-Peptidase 4 (CD26, Adenosine Deaminase Complexing Protein 2) (Dpp-IV-Wt) Complex with Bms-767778 Aka 2-(3- (Aminomethyl)-4-(2,4- Dichlorophenyl)-2-Methyl-5-Oxo-5,7-Dihydro-6H- Pyrrolo[3,4- B]Pyridin-6-Yl)-N,N-Dimethylacetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl801

b:21.9
occ:1.00
 CL2 B:1MD801 0.0 21.9 1.0
C19 B:1MD801 1.7 21.9 1.0
C20 B:1MD801 2.6 21.9 1.0
C18 B:1MD801 2.7 21.9 1.0
CG2 B:VAL656 3.5 26.4 1.0
C21 B:1MD801 3.9 21.9 1.0
OG B:SER630 3.9 29.6 1.0
N B:TYR631 4.0 28.4 1.0
C17 B:1MD801 4.0 21.9 1.0
CE2 B:TYR662 4.0 43.9 1.0
CZ B:TYR662 4.1 45.6 1.0
CA B:TYR631 4.1 29.9 1.0
CB B:TYR631 4.2 30.9 1.0
CD2 B:TYR631 4.2 30.9 1.0
CH2 B:TRP659 4.3 26.3 1.0
CZ3 B:TRP659 4.3 26.3 1.0
CD2 B:TYR662 4.3 41.9 1.0
CE1 B:TYR662 4.4 44.1 1.0
CB B:VAL656 4.4 28.1 1.0
OH B:TYR662 4.5 42.1 1.0
C14 B:1MD801 4.5 21.9 1.0
CG2 B:VAL711 4.6 22.1 1.0
CE1 B:TYR666 4.6 24.4 1.0
C B:SER630 4.6 29.3 1.0
CG B:TYR662 4.7 42.7 1.0
CD1 B:TYR662 4.7 40.8 1.0
CG B:TYR631 4.7 29.9 1.0
CZ B:TYR666 4.9 26.6 1.0
OH B:TYR666 5.0 31.9 1.0

Reference:

P.Devasthale, Y.Wang, W.Wang, J.Fevig, J.Feng, A.Wang, T.Harrity, D.Egan, N.Morgan, M.Cap, A.Fura, H.E.Klei, K.Kish, C.Weigelt, L.Sun, P.Levesque, F.Moulin, Y.X.Li, R.Zahler, M.S.Kirby, L.G.Hamann. Optimization of Activity, Selectivity, and Liability Profiles in 5-Oxopyrrolopyridine DPP4 Inhibitors Leading to Clinical Candidate (Sa)-2-(3-(Aminomethyl)-4-(2,4-Dichlorophenyl)-2-Methyl-5- Oxo-5H-Pyrrolo[3,4-B]Pyridin-6(7H)-Yl)-N,N-Dimethylacetamide (Bms-767778). J.Med.Chem. V. 56 7343 2013.
ISSN: ISSN 0022-2623
PubMed: 23964740
DOI: 10.1021/JM4008906
Page generated: Sun Jul 21 17:26:31 2024

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