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Chlorine in PDB 5sfg: Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- (Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- (Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- (Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- (Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide, PDB code: 5sfg was solved by C.Joseph, K.Groebke-Zbinden, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.79 / 2.31
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.146, 136.146, 235.981, 90, 90, 120
R / Rfree (%) 16 / 19.5

Other elements in 5sfg:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- (Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Magnesium (Mg) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- (Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide (pdb code 5sfg). 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 Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- (Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide, PDB code: 5sfg:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5sfg

Go back to Chlorine Binding Sites List in 5sfg
Chlorine binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- (Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide


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 Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- (Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl803

b:40.5
occ:1.00
 CL29 A:IKK803 0.0 40.5 1.0
C27 A:IKK803 1.7 37.7 1.0
C26 A:IKK803 2.7 37.4 1.0
C28 A:IKK803 2.8 37.5 1.0
O A:GLU721 3.4 45.8 1.0
CB A:GLU721 3.4 46.2 1.0
C A:GLU721 3.6 44.4 1.0
N A:MET713 3.7 43.8 1.0
C A:PRO712 3.8 45.4 1.0
CB A:PRO712 3.9 47.6 1.0
CA A:MET713 3.9 44.2 1.0
O A:PRO712 3.9 47.7 1.0
N9 A:IKK803 3.9 38.0 1.0
C24 A:IKK803 4.0 35.6 1.0
O A:LYS718 4.1 41.8 1.0
N A:VAL722 4.1 40.8 1.0
CA A:GLU721 4.2 45.5 1.0
O A:HOH990 4.2 38.0 1.0
OE1 A:GLU721 4.2 50.3 1.0
CA A:VAL722 4.3 39.2 1.0
O A:HOH933 4.3 49.6 1.0
C6 A:IKK803 4.5 36.5 1.0
CA A:PRO712 4.5 47.2 1.0
CG A:GLU721 4.6 49.3 1.0
CA A:GLY725 4.8 37.0 1.0
CB A:MET713 4.8 45.0 1.0
CD A:GLU721 4.8 51.8 1.0
CG2 A:VAL722 4.8 38.3 1.0
O A:HOH985 5.0 40.0 1.0
N A:GLU721 5.0 49.6 1.0

Chlorine binding site 2 out of 4 in 5sfg

Go back to Chlorine Binding Sites List in 5sfg
Chlorine binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- (Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide


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 Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- (Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl803

b:39.8
occ:1.00
 CL29 B:IKK803 0.0 39.8 1.0
C27 B:IKK803 1.7 38.1 1.0
C26 B:IKK803 2.7 37.6 1.0
C28 B:IKK803 2.7 37.8 1.0
O B:GLU721 3.3 40.8 1.0
CB B:GLU721 3.5 41.8 1.0
C B:GLU721 3.5 37.6 1.0
CB B:PRO712 3.8 39.3 1.0
O B:PRO712 3.8 37.5 1.0
C B:PRO712 3.8 38.0 1.0
N9 B:IKK803 3.9 35.5 1.0
O B:LYS718 3.9 43.4 1.0
N B:MET713 4.0 38.1 1.0
N B:VAL722 4.0 33.8 1.0
C24 B:IKK803 4.0 37.9 1.0
CA B:GLU721 4.1 41.0 1.0
CA B:MET713 4.2 37.8 1.0
CA B:VAL722 4.3 35.4 1.0
C6 B:IKK803 4.4 36.6 1.0
CA B:PRO712 4.5 38.6 1.0
OE1 B:GLU721 4.7 48.8 1.0
CG B:GLU721 4.8 43.9 1.0
CG2 B:VAL722 4.8 36.0 1.0
N B:GLU721 4.8 41.2 1.0
CB B:LYS718 4.9 45.3 1.0
CA B:GLY725 4.9 36.3 1.0
CD B:GLU721 5.0 47.0 1.0

Chlorine binding site 3 out of 4 in 5sfg

Go back to Chlorine Binding Sites List in 5sfg
Chlorine binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- (Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide


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 Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- (Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl803

b:44.6
occ:1.00
 CL29 C:IKK803 0.0 44.6 1.0
C27 C:IKK803 1.7 42.2 1.0
C28 C:IKK803 2.7 42.7 1.0
C26 C:IKK803 2.7 42.0 1.0
O C:GLU721 3.4 46.3 1.0
CB C:GLU721 3.6 45.6 1.0
C C:GLU721 3.6 44.5 1.0
O C:PRO712 3.8 41.2 1.0
C C:PRO712 3.9 41.1 1.0
CA C:MET713 3.9 38.1 1.0
N C:MET713 3.9 37.5 1.0
N9 C:IKK803 3.9 40.8 1.0
C24 C:IKK803 4.0 41.6 1.0
N C:VAL722 4.0 43.6 1.0
CB C:PRO712 4.0 44.6 1.0
CA C:VAL722 4.2 43.8 1.0
O C:LYS718 4.2 45.9 1.0
CA C:GLU721 4.2 44.6 1.0
C6 C:IKK803 4.4 42.2 1.0
CA C:PRO712 4.6 41.9 1.0
CB C:MET713 4.6 39.9 1.0
CG2 C:VAL722 4.6 39.9 1.0
CA C:GLY725 4.7 39.8 1.0
OE1 C:GLU721 4.8 51.2 1.0
CG C:GLU721 4.9 47.8 1.0
N C:GLY725 4.9 40.3 1.0
N C:GLU721 5.0 44.4 1.0

Chlorine binding site 4 out of 4 in 5sfg

Go back to Chlorine Binding Sites List in 5sfg
Chlorine binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- (Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide


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 Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- (Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl803

b:50.0
occ:1.00
 CL29 D:IKK803 0.0 50.0 1.0
C27 D:IKK803 1.7 48.0 1.0
C26 D:IKK803 2.7 46.9 1.0
C28 D:IKK803 2.7 48.9 1.0
O D:GLU721 3.1 50.0 1.0
CB D:GLU721 3.5 50.8 1.0
C D:GLU721 3.6 48.5 1.0
CB D:PRO712 3.6 48.3 1.0
C D:PRO712 3.7 44.8 1.0
N D:MET713 3.8 46.4 1.0
O D:PRO712 3.8 45.7 1.0
N9 D:IKK803 3.9 49.8 1.0
C24 D:IKK803 4.0 48.4 1.0
CA D:MET713 4.0 49.1 1.0
N D:VAL722 4.1 45.4 1.0
O D:LYS718 4.2 47.8 1.0
CA D:GLU721 4.2 49.4 1.0
CA D:PRO712 4.3 48.1 1.0
CA D:VAL722 4.4 44.5 1.0
C6 D:IKK803 4.4 48.0 1.0
OE1 D:GLU721 4.4 50.0 1.0
CG D:GLU721 4.8 52.9 1.0
CA D:GLY725 4.8 40.8 1.0
CG D:PRO712 4.9 48.6 1.0
CD D:GLU721 5.0 53.9 1.0
CB D:LYS718 5.0 51.0 1.0
C D:MET713 5.0 49.6 1.0

Reference:

A.Tosstorff, M.G.Rudolph, J.C.Cole, M.Reutlinger, C.Kramer, H.Schaffhauser, A.Nilly, A.Flohr, B.Kuhn. A High Quality, Industrial Data Set For Binding Affinity Prediction: Performance Comparison in Different Early Drug Discovery Scenarios. J.Comput.Aided Mol.Des. V. 36 753 2022.
ISSN: ESSN 1573-4951
PubMed: 36153472
DOI: 10.1007/S10822-022-00478-X
Page generated: Fri Jul 26 16:47:49 2024

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