Atomistry » Chlorine » PDB 5sdd-5sil » 5sfg
Atomistry »
  Chlorine »
    PDB 5sdd-5sil »
      5sfg »

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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy