scPDB - 3g0g entry

Protein Data Bank Entry:

PDB ID : 3g0g

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2009-01-27

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
B	100 %

Ligand binding site composition:

B-Factor:	36.910
Number of residues:	28
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.361	324.000

% Hydrophobic	% Polar
33.33	66.67
According to VolSite

Ligand :

HET Code:	RUM
Formula:	C17H19BrN5O
Molecular weight:	389.270 g/mol
DrugBank ID:	-
Buried Surface Area:	61.19 %
Polar Surface area:	87.34 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
1.06712	-11.7957	21.4609

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
N24	OE1	GLU- 205	2.81	160.47	H-Bond (Ligand Donor)	false
N24	OE1	GLU- 205	2.81	0	Ionic (Ligand Cationic)	false
N24	OE2	GLU- 206	3.72	0	Ionic (Ligand Cationic)	false
N24	OE1	GLU- 206	3.09	0	Ionic (Ligand Cationic)	false
N24	OE1	GLU- 206	3.09	166.33	H-Bond (Ligand Donor)	false
C20	CE1	PHE- 357	4.03	0	Hydrophobic	false
C9	CE1	TYR- 547	4.49	0	Hydrophobic	false
BR7	CD1	TYR- 547	3.63	0	Hydrophobic	false
BR7	CB	SER- 630	3.9	0	Hydrophobic	false
C14	CB	SER- 630	3.61	0	Hydrophobic	false
O8	N	TYR- 631	3.1	156.53	H-Bond (Protein Donor)	false
C11	CB	TYR- 631	3.83	0	Hydrophobic	false
C13	CG2	VAL- 656	3.61	0	Hydrophobic	false
C13	CZ	TYR- 662	3.46	0	Hydrophobic	false
C9	CE1	TYR- 666	3.61	0	Hydrophobic	false
C20	CE1	TYR- 666	4.17	0	Hydrophobic	false
N17	ND2	ASN- 710	3.34	126.56	H-Bond (Protein Donor)	false
C14	CG2	VAL- 711	3.53	0	Hydrophobic	false
N24	O	HOH- 1202	2.59	120.86	H-Bond (Ligand Donor)	false