scPDB - 4dtc entry

Protein Data Bank Entry:

PDB ID : 4dtc

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2012-02-21

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:	85.515
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.574	546.750

% Hydrophobic	% Polar
33.95	66.05
According to VolSite

Ligand :

HET Code:	D5C
Formula:	C24H21F6N2O
Molecular weight:	467.427 g/mol
DrugBank ID:	-
Buried Surface Area:	56.65 %
Polar Surface area:	56.74 Å2

Number of
H-Bond Acceptors:	1
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-11.48	9.67297	26.4504

Binding mode :

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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
CAL	CG	GLU- 205	4.36	0	Hydrophobic	false
NAM	OE2	GLU- 205	2.78	163.23	H-Bond (Ligand Donor)	false
NAM	OE2	GLU- 205	2.78	0	Ionic (Ligand Cationic)	false
NAM	OE1	GLU- 206	3.52	0	Ionic (Ligand Cationic)	false
NAM	OE2	GLU- 206	2.61	0	Ionic (Ligand Cationic)	false
NAM	OE2	GLU- 206	2.61	143.61	H-Bond (Ligand Donor)	false
CAY	CB	SER- 209	4.36	0	Hydrophobic	false
CAS	CB	PHE- 357	3.55	0	Hydrophobic	false
CAT	CD	ARG- 358	4.31	0	Hydrophobic	false
FBG	CG	ARG- 358	3.5	0	Hydrophobic	false
CBC	CD	ARG- 358	3.81	0	Hydrophobic	false
FAH	CB	SER- 630	4.12	0	Hydrophobic	false
CAB	CB	TYR- 631	4.13	0	Hydrophobic	false
FAI	CD2	TYR- 631	3.35	0	Hydrophobic	false
FAI	CG2	VAL- 656	4.36	0	Hydrophobic	false
FAH	CG2	VAL- 656	3.35	0	Hydrophobic	false
FAI	CH2	TRP- 659	3.83	0	Hydrophobic	false
NAM	OH	TYR- 662	2.93	153.37	H-Bond (Ligand Donor)	false
FAH	CZ	TYR- 662	4.07	0	Hydrophobic	false
FAI	CE2	TYR- 662	4.29	0	Hydrophobic	false
CAJ	CE2	TYR- 666	4.11	0	Hydrophobic	false
FAI	CE1	TYR- 666	3.55	0	Hydrophobic	false
FAH	CG2	VAL- 711	3.28	0	Hydrophobic	false