scPDB - 3vjl entry

Protein Data Bank Entry:

PDB ID : 3vjl

Resolution :2.390 Å

Experimental Method : X-ray

Deposition Date : 2011-10-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dipeptidyl peptidase 4
ID:	DPP4_HUMAN
AC:	P27487
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.261
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.064	330.750

% Hydrophobic	% Polar
32.65	67.35
According to VolSite

Ligand :

HET Code:	W94
Formula:	C23H29F3N5OS
Molecular weight:	480.569 g/mol
DrugBank ID:	-
Buried Surface Area:	42.14 %
Polar Surface area:	83.28 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
50.797	63.2452	35.1811

Binding mode :

What is Poseview ?

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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
N25	OE1	GLU- 205	2.74	149.62	H-Bond (Ligand Donor)	false
N25	OE1	GLU- 205	2.74	0	Ionic (Ligand Cationic)	false
N25	OE2	GLU- 206	3.11	132.98	H-Bond (Ligand Donor)	false
N25	OE1	GLU- 206	2.76	164.04	H-Bond (Ligand Donor)	false
N25	OE2	GLU- 206	3.11	0	Ionic (Ligand Cationic)	false
N25	OE1	GLU- 206	2.76	0	Ionic (Ligand Cationic)	false
C16	CE2	PHE- 357	4.08	0	Hydrophobic	false
C17	CZ	PHE- 357	3.83	0	Hydrophobic	false
C10	CB	PHE- 357	4.02	0	Hydrophobic	false
C30	CD2	TYR- 631	3.78	0	Hydrophobic	false
S31	CB	TYR- 631	4.21	0	Hydrophobic	false
S31	CG2	VAL- 656	3.65	0	Hydrophobic	false
C30	CH2	TRP- 659	4.15	0	Hydrophobic	false
C30	CE1	TYR- 662	4.03	0	Hydrophobic	false
C23	CE1	TYR- 666	3.85	0	Hydrophobic	false
C30	CE2	TYR- 666	3.28	0	Hydrophobic	false
O33	ND2	ASN- 710	2.89	157.98	H-Bond (Protein Donor)	false
S31	CG2	VAL- 711	4.22	0	Hydrophobic	false