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Chlorine in PDB 3q0t: Crystal Structure of Human Dpp-IV in Complex Withsa-(+)- METHYL2-(3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-2-Methyl- 7-Oxo-5H-Pyrrolo[3,4- B]Pyridin-6(7H)-Yl)Acetate

Enzymatic activity of Crystal Structure of Human Dpp-IV in Complex Withsa-(+)- METHYL2-(3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-2-Methyl- 7-Oxo-5H-Pyrrolo[3,4- B]Pyridin-6(7H)-Yl)Acetate

All present enzymatic activity of Crystal Structure of Human Dpp-IV in Complex Withsa-(+)- METHYL2-(3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-2-Methyl- 7-Oxo-5H-Pyrrolo[3,4- B]Pyridin-6(7H)-Yl)Acetate:
3.4.14.5;

Protein crystallography data

The structure of Crystal Structure of Human Dpp-IV in Complex Withsa-(+)- METHYL2-(3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-2-Methyl- 7-Oxo-5H-Pyrrolo[3,4- B]Pyridin-6(7H)-Yl)Acetate, PDB code: 3q0t 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 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.686, 67.569, 420.978, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 26

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Dpp-IV in Complex Withsa-(+)- METHYL2-(3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-2-Methyl- 7-Oxo-5H-Pyrrolo[3,4- B]Pyridin-6(7H)-Yl)Acetate (pdb code 3q0t). 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 Withsa-(+)- METHYL2-(3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-2-Methyl- 7-Oxo-5H-Pyrrolo[3,4- B]Pyridin-6(7H)-Yl)Acetate, PDB code: 3q0t:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3q0t

Go back to Chlorine Binding Sites List in 3q0t
Chlorine binding site 1 out of 4 in the Crystal Structure of Human Dpp-IV in Complex Withsa-(+)- METHYL2-(3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-2-Methyl- 7-Oxo-5H-Pyrrolo[3,4- B]Pyridin-6(7H)-Yl)Acetate


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 Withsa-(+)- METHYL2-(3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-2-Methyl- 7-Oxo-5H-Pyrrolo[3,4- B]Pyridin-6(7H)-Yl)Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1

b:40.3
occ:1.00
 CL25 A:LGE1 0.0 40.3 1.0
C08 A:LGE1 1.7 42.0 1.0
C03 A:LGE1 2.6 36.3 1.0
C02 A:LGE1 2.7 37.6 1.0
CG2 A:VAL656 3.3 31.3 1.0
N A:TYR631 3.7 36.4 1.0
C09 A:LGE1 3.9 39.0 1.0
CA A:TYR631 3.9 31.4 1.0
CB A:TYR631 3.9 31.3 1.0
C01 A:LGE1 4.0 37.6 1.0
OG A:SER630 4.0 50.1 1.0
CD2 A:TYR631 4.2 28.2 1.0
CH2 A:TRP659 4.2 30.5 1.0
CE2 A:TYR662 4.3 35.0 1.0
CZ A:TYR662 4.3 36.9 1.0
CZ3 A:TRP659 4.3 27.8 1.0
C A:SER630 4.4 36.3 1.0
CB A:VAL656 4.4 33.8 1.0
C04 A:LGE1 4.4 41.3 1.0
CG A:TYR631 4.5 29.7 1.0
CD2 A:TYR662 4.5 36.4 1.0
CE1 A:TYR662 4.6 35.8 1.0
CG2 A:VAL711 4.6 34.0 1.0
OH A:TYR662 4.7 36.0 1.0
CE1 A:TYR666 4.8 32.1 1.0
CG A:TYR662 4.8 38.1 1.0
CD1 A:TYR662 4.8 33.1 1.0
O A:SER630 4.9 34.4 1.0
CB A:SER630 5.0 36.2 1.0

Chlorine binding site 2 out of 4 in 3q0t

Go back to Chlorine Binding Sites List in 3q0t
Chlorine binding site 2 out of 4 in the Crystal Structure of Human Dpp-IV in Complex Withsa-(+)- METHYL2-(3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-2-Methyl- 7-Oxo-5H-Pyrrolo[3,4- B]Pyridin-6(7H)-Yl)Acetate


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 Withsa-(+)- METHYL2-(3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-2-Methyl- 7-Oxo-5H-Pyrrolo[3,4- B]Pyridin-6(7H)-Yl)Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1

b:46.0
occ:1.00
 CL26 A:LGE1 0.0 46.0 1.0
C09 A:LGE1 1.7 39.0 1.0
C03 A:LGE1 2.6 36.3 1.0
C04 A:LGE1 2.7 41.3 1.0
C05 A:LGE1 3.0 38.7 1.0
ND2 A:ASN710 3.1 30.6 1.0
OH A:TYR662 3.3 36.0 1.0
N21 A:LGE1 3.4 37.9 1.0
C06 A:LGE1 3.5 41.4 1.0
OG A:SER630 3.6 50.1 1.0
CG A:ASN710 3.6 33.5 1.0
OD1 A:ASN710 3.6 34.3 1.0
C07 A:LGE1 3.7 35.9 1.0
NE2 A:HIS740 3.7 37.5 1.0
CD2 A:HIS740 3.8 36.6 1.0
NH2 A:ARG125 3.8 33.6 1.0
OE2 A:GLU205 3.8 26.3 1.0
C14 A:LGE1 3.9 43.0 1.0
C08 A:LGE1 3.9 42.0 1.0
C01 A:LGE1 4.0 37.6 1.0
C17 A:LGE1 4.1 37.2 1.0
CZ A:TYR662 4.4 36.9 1.0
C10 A:LGE1 4.4 37.6 1.0
C02 A:LGE1 4.5 37.6 1.0
O A:HOH895 4.6 25.0 1.0
CE1 A:HIS740 4.6 33.0 1.0
C11 A:LGE1 4.6 39.6 1.0
CG A:HIS740 4.6 34.5 1.0
CG2 A:VAL711 4.7 34.0 1.0
CB A:SER630 4.8 36.2 1.0
CB A:ASN710 4.8 29.9 1.0
CE1 A:TYR662 4.8 35.8 1.0
CD A:GLU205 4.9 34.9 1.0
N19 A:LGE1 5.0 38.6 1.0
N20 A:LGE1 5.0 39.4 1.0

Chlorine binding site 3 out of 4 in 3q0t

Go back to Chlorine Binding Sites List in 3q0t
Chlorine binding site 3 out of 4 in the Crystal Structure of Human Dpp-IV in Complex Withsa-(+)- METHYL2-(3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-2-Methyl- 7-Oxo-5H-Pyrrolo[3,4- B]Pyridin-6(7H)-Yl)Acetate


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 Withsa-(+)- METHYL2-(3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-2-Methyl- 7-Oxo-5H-Pyrrolo[3,4- B]Pyridin-6(7H)-Yl)Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2

b:40.7
occ:1.00
 CL25 B:LGE2 0.0 40.7 1.0
C08 B:LGE2 1.7 44.5 1.0
C03 B:LGE2 2.6 37.9 1.0
C02 B:LGE2 2.7 37.8 1.0
CG2 B:VAL656 3.4 33.3 1.0
OG B:SER630 3.9 44.3 1.0
C09 B:LGE2 3.9 40.0 1.0
N B:TYR631 3.9 38.0 1.0
C01 B:LGE2 4.0 39.1 1.0
CH2 B:TRP659 4.0 34.7 1.0
CA B:TYR631 4.1 38.6 1.0
CD2 B:TYR631 4.1 30.6 1.0
CB B:TYR631 4.2 31.9 1.0
CZ B:TYR662 4.2 41.0 1.0
CE2 B:TYR662 4.2 37.9 1.0
CZ3 B:TRP659 4.3 33.7 1.0
CB B:VAL656 4.4 38.7 1.0
C04 B:LGE2 4.5 43.1 1.0
C B:SER630 4.5 37.5 1.0
CG2 B:VAL711 4.5 29.4 1.0
CE1 B:TYR662 4.5 38.1 1.0
CD2 B:TYR662 4.5 35.9 1.0
OH B:TYR662 4.6 41.1 1.0
CG B:TYR631 4.6 28.6 1.0
CE1 B:TYR666 4.8 37.8 1.0
CD1 B:TYR662 4.8 34.1 1.0
CG B:TYR662 4.8 37.9 1.0
O B:SER630 4.9 37.6 1.0
CB B:SER630 5.0 36.6 1.0

Chlorine binding site 4 out of 4 in 3q0t

Go back to Chlorine Binding Sites List in 3q0t
Chlorine binding site 4 out of 4 in the Crystal Structure of Human Dpp-IV in Complex Withsa-(+)- METHYL2-(3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-2-Methyl- 7-Oxo-5H-Pyrrolo[3,4- B]Pyridin-6(7H)-Yl)Acetate


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 Withsa-(+)- METHYL2-(3- (Aminomethyl)-4-(2,4-Dichlorophenyl)-2-Methyl- 7-Oxo-5H-Pyrrolo[3,4- B]Pyridin-6(7H)-Yl)Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2

b:40.9
occ:1.00
 CL26 B:LGE2 0.0 40.9 1.0
C09 B:LGE2 1.7 40.0 1.0
C03 B:LGE2 2.7 37.9 1.0
C04 B:LGE2 2.7 43.1 1.0
C05 B:LGE2 3.0 39.8 1.0
ND2 B:ASN710 3.2 33.7 1.0
OH B:TYR662 3.3 41.1 1.0
C06 B:LGE2 3.4 43.1 1.0
N21 B:LGE2 3.6 32.9 1.0
NH2 B:ARG125 3.6 34.3 1.0
NE2 B:HIS740 3.6 37.2 1.0
C14 B:LGE2 3.7 40.0 1.0
OG B:SER630 3.8 44.3 1.0
CG B:ASN710 3.8 37.5 1.0
CD2 B:HIS740 3.8 32.7 1.0
C07 B:LGE2 3.8 32.0 1.0
OE2 B:GLU205 3.9 29.8 1.0
OD1 B:ASN710 3.9 39.4 1.0
C08 B:LGE2 3.9 44.5 1.0
C01 B:LGE2 4.0 39.1 1.0
C17 B:LGE2 4.3 31.9 1.0
O B:HOH819 4.4 25.0 1.0
C10 B:LGE2 4.4 38.6 1.0
CE1 B:HIS740 4.4 36.8 1.0
C02 B:LGE2 4.5 37.8 1.0
CZ B:TYR662 4.5 41.0 1.0
CG B:HIS740 4.6 32.9 1.0
C11 B:LGE2 4.7 39.1 1.0
CG2 B:VAL711 4.7 29.4 1.0
N20 B:LGE2 4.8 45.4 1.0
CB B:ASN710 4.8 32.2 1.0
CB B:SER630 4.9 36.6 1.0
ND1 B:HIS740 4.9 39.0 1.0
CZ B:ARG125 4.9 39.5 1.0
N19 B:LGE2 5.0 36.7 1.0

Reference:

W.Wang, P.Devasthale, A.Wang, D.Egan, N.Morgan, M.Cap, A.Fura, H.E.Klei, K.Kish, L.Sun, P.Levesque, R.Zahler, M.Kirby, L.G.Hamann. Discovery of 7-Oxo-Pyrrolopyridines As Potent and Selective Inhibitors of DPP4 To Be Published.
Page generated: Sun Jul 21 02:40:15 2024

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