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Chlorine in PDB 3sww: Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-6-(2-Methoxyphenyl)- 2-Methyl- 5H-Pyrrolo[3,4-B]Pyridin-7(6H)-One

Enzymatic activity of Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-6-(2-Methoxyphenyl)- 2-Methyl- 5H-Pyrrolo[3,4-B]Pyridin-7(6H)-One

All present enzymatic activity of Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-6-(2-Methoxyphenyl)- 2-Methyl- 5H-Pyrrolo[3,4-B]Pyridin-7(6H)-One:
3.4.14.5;

Protein crystallography data

The structure of Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-6-(2-Methoxyphenyl)- 2-Methyl- 5H-Pyrrolo[3,4-B]Pyridin-7(6H)-One, PDB code: 3sww 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) 47.16 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.534, 67.928, 423.472, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-6-(2-Methoxyphenyl)- 2-Methyl- 5H-Pyrrolo[3,4-B]Pyridin-7(6H)-One (pdb code 3sww). 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 Human Dpp-IV in Complex with Sa-(+)-3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-6-(2-Methoxyphenyl)- 2-Methyl- 5H-Pyrrolo[3,4-B]Pyridin-7(6H)-One, PDB code: 3sww:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3sww

Go back to Chlorine Binding Sites List in 3sww
Chlorine binding site 1 out of 4 in the Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-6-(2-Methoxyphenyl)- 2-Methyl- 5H-Pyrrolo[3,4-B]Pyridin-7(6H)-One


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 Human Dpp-IV in Complex with Sa-(+)-3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-6-(2-Methoxyphenyl)- 2-Methyl- 5H-Pyrrolo[3,4-B]Pyridin-7(6H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1

b:34.4
occ:1.00
 CL1 A:KXB1 0.0 34.4 1.0
C08 A:KXB1 1.7 30.4 1.0
C03 A:KXB1 2.6 28.1 1.0
C02 A:KXB1 2.7 25.7 1.0
CG2 A:VAL656 3.3 22.9 1.0
C09 A:KXB1 3.9 31.2 1.0
CH2 A:TRP659 3.9 24.1 1.0
C01 A:KXB1 3.9 27.1 1.0
N A:TYR631 3.9 26.9 1.0
CE2 A:TYR662 4.0 27.3 1.0
CZ3 A:TRP659 4.1 25.0 1.0
CA A:TYR631 4.1 25.0 1.0
CD2 A:TYR631 4.2 27.5 1.0
CB A:TYR631 4.2 23.5 1.0
CD2 A:TYR662 4.2 24.4 1.0
CZ A:TYR662 4.2 26.7 1.0
OG A:SER630 4.2 34.3 1.0
CB A:VAL656 4.4 25.9 1.0
C04 A:KXB1 4.4 29.4 1.0
C A:SER630 4.5 26.9 1.0
CG A:TYR662 4.6 26.2 1.0
CG2 A:VAL711 4.6 25.0 1.0
CE1 A:TYR662 4.6 24.1 1.0
CE1 A:TYR666 4.6 25.1 1.0
CG A:TYR631 4.7 25.5 1.0
OH A:TYR662 4.7 25.8 1.0
CD1 A:TYR662 4.7 22.5 1.0

Chlorine binding site 2 out of 4 in 3sww

Go back to Chlorine Binding Sites List in 3sww
Chlorine binding site 2 out of 4 in the Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-6-(2-Methoxyphenyl)- 2-Methyl- 5H-Pyrrolo[3,4-B]Pyridin-7(6H)-One


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 Human Dpp-IV in Complex with Sa-(+)-3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-6-(2-Methoxyphenyl)- 2-Methyl- 5H-Pyrrolo[3,4-B]Pyridin-7(6H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1

b:37.9
occ:1.00
 CL2 A:KXB1 0.0 37.9 1.0
C09 A:KXB1 1.7 31.2 1.0
C03 A:KXB1 2.6 28.1 1.0
C04 A:KXB1 2.7 29.4 1.0
C05 A:KXB1 3.0 30.7 1.0
ND2 A:ASN710 3.3 24.4 1.0
C06 A:KXB1 3.4 33.6 1.0
OH A:TYR662 3.4 25.8 1.0
NE2 A:HIS740 3.5 27.0 1.0
OG A:SER630 3.6 34.3 1.0
N21 A:KXB1 3.6 27.1 1.0
CD2 A:HIS740 3.6 29.2 1.0
CG A:ASN710 3.7 26.9 1.0
C13 A:KXB1 3.7 36.1 1.0
OD1 A:ASN710 3.7 24.8 1.0
C07 A:KXB1 3.7 27.6 1.0
NH2 A:ARG125 3.7 27.2 1.0
C08 A:KXB1 3.9 30.4 1.0
OE2 A:GLU205 3.9 26.0 1.0
C01 A:KXB1 4.0 27.1 1.0
C16 A:KXB1 4.2 28.0 1.0
C10 A:KXB1 4.3 32.3 1.0
O A:HOH793 4.3 24.0 1.0
CE1 A:HIS740 4.4 30.7 1.0
C02 A:KXB1 4.5 25.7 1.0
CZ A:TYR662 4.5 26.7 1.0
CG A:HIS740 4.5 25.3 1.0
C11 A:KXB1 4.6 30.4 1.0
CB A:ASN710 4.7 22.0 1.0
CG2 A:VAL711 4.7 25.0 1.0
N20 A:KXB1 4.8 36.6 1.0
CB A:SER630 4.8 28.3 1.0
N19 A:KXB1 4.9 31.7 1.0
ND1 A:HIS740 4.9 23.5 1.0

Chlorine binding site 3 out of 4 in 3sww

Go back to Chlorine Binding Sites List in 3sww
Chlorine binding site 3 out of 4 in the Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-6-(2-Methoxyphenyl)- 2-Methyl- 5H-Pyrrolo[3,4-B]Pyridin-7(6H)-One


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 Human Dpp-IV in Complex with Sa-(+)-3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-6-(2-Methoxyphenyl)- 2-Methyl- 5H-Pyrrolo[3,4-B]Pyridin-7(6H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2

b:35.4
occ:1.00
 CL1 B:KXB2 0.0 35.4 1.0
C08 B:KXB2 1.7 33.8 1.0
C03 B:KXB2 2.6 33.8 1.0
C02 B:KXB2 2.7 26.9 1.0
CG2 B:VAL656 3.3 24.2 1.0
C09 B:KXB2 3.9 31.5 1.0
C01 B:KXB2 3.9 31.4 1.0
N B:TYR631 4.0 29.1 1.0
CH2 B:TRP659 4.0 27.6 1.0
CE2 B:TYR662 4.0 25.7 1.0
CA B:TYR631 4.1 27.2 1.0
CZ3 B:TRP659 4.1 25.7 1.0
OG B:SER630 4.2 35.8 1.0
CZ B:TYR662 4.2 28.0 1.0
CD2 B:TYR662 4.3 27.6 1.0
CB B:TYR631 4.3 26.2 1.0
CD2 B:TYR631 4.3 23.4 1.0
CB B:VAL656 4.3 26.2 1.0
C04 B:KXB2 4.4 32.6 1.0
C B:SER630 4.5 30.1 1.0
CE1 B:TYR662 4.5 23.1 1.0
CG2 B:VAL711 4.5 24.8 1.0
CE1 B:TYR666 4.6 25.2 1.0
CG B:TYR662 4.6 25.6 1.0
OH B:TYR662 4.6 26.1 1.0
CD1 B:TYR662 4.7 24.0 1.0
CG B:TYR631 4.7 24.1 1.0
O B:SER630 4.9 28.6 1.0
CZ B:TYR666 5.0 29.4 1.0

Chlorine binding site 4 out of 4 in 3sww

Go back to Chlorine Binding Sites List in 3sww
Chlorine binding site 4 out of 4 in the Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-6-(2-Methoxyphenyl)- 2-Methyl- 5H-Pyrrolo[3,4-B]Pyridin-7(6H)-One


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 Human Dpp-IV in Complex with Sa-(+)-3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-6-(2-Methoxyphenyl)- 2-Methyl- 5H-Pyrrolo[3,4-B]Pyridin-7(6H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2

b:40.4
occ:1.00
 CL2 B:KXB2 0.0 40.4 1.0
C09 B:KXB2 1.7 31.5 1.0
C03 B:KXB2 2.6 33.8 1.0
C04 B:KXB2 2.7 32.6 1.0
C05 B:KXB2 3.1 32.7 1.0
ND2 B:ASN710 3.3 24.6 1.0
C06 B:KXB2 3.4 35.3 1.0
NE2 B:HIS740 3.5 27.4 1.0
CD2 B:HIS740 3.5 26.6 1.0
OH B:TYR662 3.5 26.1 1.0
OD1 B:ASN710 3.7 26.8 1.0
CG B:ASN710 3.7 26.2 1.0
OG B:SER630 3.7 35.8 1.0
N21 B:KXB2 3.7 23.6 1.0
C13 B:KXB2 3.7 31.5 1.0
NH2 B:ARG125 3.7 29.2 1.0
C07 B:KXB2 3.8 30.8 1.0
C08 B:KXB2 3.9 33.8 1.0
OE2 B:GLU205 4.0 28.9 1.0
C01 B:KXB2 4.0 31.4 1.0
C16 B:KXB2 4.4 28.2 1.0
CE1 B:HIS740 4.4 27.8 1.0
C10 B:KXB2 4.4 33.8 1.0
CG B:HIS740 4.4 27.1 1.0
O B:HOH17 4.4 25.8 1.0
C02 B:KXB2 4.5 26.9 1.0
CZ B:TYR662 4.6 28.0 1.0
CG2 B:VAL711 4.7 24.8 1.0
C11 B:KXB2 4.7 29.4 1.0
CB B:ASN710 4.8 23.1 1.0
CB B:SER630 4.8 28.8 1.0
N20 B:KXB2 4.8 39.1 1.0
ND1 B:HIS740 4.9 24.1 1.0

Reference:

W.Wang, P.Devasthale, A.Wang, T.Harrity, D.Egan, N.Morgan, M.Cap, A.Fura, H.E.Klei, K.Kish, C.Weigelt, L.Sun, P.Levesque, Y.X.Li, R.Zahler, M.S.Kirby, L.G.Hamann. 7-Oxopyrrolopyridine-Derived DPP4 Inhibitors-Mitigation of Cyp and Herg Liabilities Via Introduction of Polar Functionalities in the Active Site. Bioorg.Med.Chem.Lett. V. 21 6646 2011.
ISSN: ISSN 0960-894X
PubMed: 21996520
DOI: 10.1016/J.BMCL.2011.09.074
Page generated: Sun Jul 21 04:51:05 2024

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