scPDB - 3ccb entry

Protein Data Bank Entry:

PDB ID : 3ccb

Resolution :2.490 Å

Experimental Method : X-ray

Deposition Date : 2008-02-25

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
C	100 %

Ligand binding site composition:

B-Factor:	43.891
Number of residues:	20
Including
Standard Amino Acids:	18
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.112	354.375

% Hydrophobic	% Polar
35.24	64.76
According to VolSite

Ligand :

HET Code:	B2Y
Formula:	C13H14N
Molecular weight:	184.257 g/mol
DrugBank ID:	DB07412
Buried Surface Area:	60.44 %
Polar Surface area:	27.64 Å2

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

Mass center Coordinates

X	Y	Z
-44.2369	-3.49036	-31.1002

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
N1	OE1	GLU- 205	2.71	158.23	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 205	2.71	0	Ionic (Ligand Cationic)	false
N1	OE1	GLU- 206	3.06	144.28	H-Bond (Ligand Donor)	false
N1	OE2	GLU- 206	2.72	138.58	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 206	3.06	0	Ionic (Ligand Cationic)	false
N1	OE2	GLU- 206	2.72	0	Ionic (Ligand Cationic)	false
C11	CB	SER- 630	3.73	0	Hydrophobic	false
C13	CB	TYR- 631	4.16	0	Hydrophobic	false
C12	CG2	VAL- 656	4.1	0	Hydrophobic	false
N1	OH	TYR- 662	3.08	150.39	H-Bond (Ligand Donor)	false
C11	CZ	TYR- 662	3.48	0	Hydrophobic	false
C11	CG2	VAL- 711	3.48	0	Hydrophobic	false