scPDB - 4a5s entry

Protein Data Bank Entry:

PDB ID : 4a5s

Resolution :1.620 Å

Experimental Method : X-ray

Deposition Date : 2011-10-28

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:	15.667
Number of residues:	35
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.275	648.000

% Hydrophobic	% Polar
30.73	69.27
According to VolSite

Ligand :

HET Code:	N7F
Formula:	C29H28N7O
Molecular weight:	490.579 g/mol
DrugBank ID:	-
Buried Surface Area:	58.86 %
Polar Surface area:	105.16 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
25.8946	66.7941	82.9685

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
N18	OE2	GLU- 205	2.74	170.2	H-Bond (Ligand Donor)	false
N18	OE2	GLU- 205	2.74	0	Ionic (Ligand Cationic)	false
N18	OE1	GLU- 206	3.31	138.86	H-Bond (Ligand Donor)	false
N18	OE2	GLU- 206	2.68	159.15	H-Bond (Ligand Donor)	false
N18	OE1	GLU- 206	3.31	0	Ionic (Ligand Cationic)	false
N18	OE2	GLU- 206	2.68	0	Ionic (Ligand Cationic)	false
C16	CD2	PHE- 357	4.11	0	Hydrophobic	false
C17	CE2	PHE- 357	4.26	0	Hydrophobic	false
C19	CE1	TYR- 547	3.97	0	Hydrophobic	false
C27	CG	TYR- 547	3.63	0	Hydrophobic	false
C28	CB	TYR- 547	4.41	0	Hydrophobic	false
C30	CZ2	TRP- 627	3.42	0	Hydrophobic	false
C31	CB	TRP- 629	3.74	0	Hydrophobic	false
C33	CB	TRP- 629	3.58	0	Hydrophobic	false
C27	CB	SER- 630	4.48	0	Hydrophobic	false
C37	CB	SER- 630	4.45	0	Hydrophobic	false
C22	CB	SER- 630	3.46	0	Hydrophobic	false
O26	N	TYR- 631	2.99	142.13	H-Bond (Protein Donor)	false
C20	CB	TYR- 631	4.08	0	Hydrophobic	false
C25	CB	TYR- 631	3.85	0	Hydrophobic	false
C23	CG2	VAL- 656	3.78	0	Hydrophobic	false
N18	OH	TYR- 662	2.81	134.4	H-Bond (Ligand Donor)	false
C23	CZ	TYR- 662	3.36	0	Hydrophobic	false
C19	CZ	TYR- 666	4.28	0	Hydrophobic	false
C15	CD1	TYR- 666	4.34	0	Hydrophobic	false
C23	CG2	VAL- 711	3.57	0	Hydrophobic	false