scPDB - 3tc5 entry

Protein Data Bank Entry:

PDB ID : 3tc5

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2011-08-08

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:	18.516
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.067	354.375

% Hydrophobic	% Polar
46.67	53.33
According to VolSite

Ligand :

HET Code:	3T5
Formula:	C22H28FO8P
Molecular weight:	470.425 g/mol
DrugBank ID:	-
Buried Surface Area:	57.05 %
Polar Surface area:	156.82 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	4
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
38.5253	-13.8379	15.7448

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
O8	NZ	LYS- 63	2.72	170.41	H-Bond (Protein Donor)	false
O8	NZ	LYS- 63	2.72	0	Ionic (Protein Cationic)	false
O6	CZ	ARG- 68	3.6	0	Ionic (Protein Cationic)	false
O7	CZ	ARG- 68	3.75	0	Ionic (Protein Cationic)	false
O6	NE	ARG- 68	2.78	151.35	H-Bond (Protein Donor)	false
O7	NH1	ARG- 68	3.02	156.56	H-Bond (Protein Donor)	false
O8	CZ	ARG- 69	3.35	0	Ionic (Protein Cationic)	false
C1	SG	CYS- 113	4.39	0	Hydrophobic	false
C1	CD2	LEU- 122	3.86	0	Hydrophobic	false
C8	CB	LEU- 122	4.18	0	Hydrophobic	false
C18	CD1	LEU- 122	4.24	0	Hydrophobic	false
C16	CD1	LEU- 122	4.17	0	Hydrophobic	false
C14	CD2	PHE- 125	3.53	0	Hydrophobic	false
F	CB	MET- 130	3.74	0	Hydrophobic	false
C14	SD	MET- 130	4.08	0	Hydrophobic	false
C15	CB	MET- 130	3.77	0	Hydrophobic	false
C17	CB	MET- 130	4.46	0	Hydrophobic	false
O3	NE2	GLN- 131	3.06	156.63	H-Bond (Protein Donor)	false
C20	CB	GLN- 131	4.21	0	Hydrophobic	false
C15	CE1	PHE- 134	4.17	0	Hydrophobic	false
C20	CD2	PHE- 134	3.74	0	Hydrophobic	false
C20	CG2	THR- 152	4.35	0	Hydrophobic	false
O6	OG	SER- 154	2.72	146.37	H-Bond (Protein Donor)	false
C23	CB	SER- 154	4.12	0	Hydrophobic	false
O6	O	HOH- 216	2.72	165.74	H-Bond (Protein Donor)	false