scPDB - 3odk entry

Protein Data Bank Entry:

PDB ID : 3odk

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2010-08-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
ID:	PIN1_HUMAN
AC:	Q13526
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	5.2.1.8

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	48.805
Number of residues:	20
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.098	300.375

% Hydrophobic	% Polar
46.07	53.93
According to VolSite

Ligand :

HET Code:	ODK
Formula:	C9H6N3O2
Molecular weight:	188.163 g/mol
DrugBank ID:	-
Buried Surface Area:	56.09 %
Polar Surface area:	81.7 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
39.0816	-16.4769	11.9753

Binding mode :

What is Poseview ?

2D View
3D View

Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O9	NZ	LYS- 63	3.04	146.43	H-Bond (Protein Donor)	false
O9	NZ	LYS- 63	3.04	0	Ionic (Protein Cationic)	false
C12	CD1	LEU- 122	4.38	0	Hydrophobic	false
C13	CB	MET- 130	4.31	0	Hydrophobic	false
C14	SD	MET- 130	3.6	0	Hydrophobic	false
C13	CB	GLN- 131	4.12	0	Hydrophobic	false
C13	CB	PHE- 134	3.74	0	Hydrophobic	false
N8	OG	SER- 154	3.12	160.8	H-Bond (Protein Donor)	false