scPDB - 3p5s entry

Protein Data Bank Entry:

PDB ID : 3p5s

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2010-10-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	CD38 molecule
ID:	Q9TTF5_BOVIN
AC:	Q9TTF5
Organism:	Bos taurus
Reign:	Eukaryota
TaxID:	9913
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	37.363
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.510	570.375

% Hydrophobic	% Polar
56.21	43.79
According to VolSite

Ligand :

HET Code:	AVU
Formula:	C15H20FN5O12P2
Molecular weight:	543.292 g/mol
DrugBank ID:	-
Buried Surface Area:	63.7 %
Polar Surface area:	276.33 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
19.7727	-3.36366	-0.164057

Binding mode :

What is Poseview ?

2D View
3D View

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
O3R	O	TRP- 118	2.95	125.93	H-Bond (Ligand Donor)	false
O3R	N	TRP- 118	3.06	176.5	H-Bond (Protein Donor)	false
C5R	CZ3	TRP- 118	3.56	0	Hydrophobic	false
F2R	CE2	TRP- 118	3.77	0	Hydrophobic	false
O2B	OG	SER- 119	2.63	162.54	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 120	3.03	132.57	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 120	3.03	0	Ionic (Protein Cationic)	false
F2R	CD2	LEU- 137	3.52	0	Hydrophobic	false
N6	OE2	GLU- 138	2.78	147.82	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 147	3.2	131.75	H-Bond (Ligand Donor)	false
N1	N	GLY- 148	3.34	168.7	H-Bond (Protein Donor)	false
C1R	CB	SER- 185	3.94	0	Hydrophobic	false
O1B	N	ILE- 213	2.69	128.48	H-Bond (Protein Donor)	false
C1R	CG2	ILE- 213	4.08	0	Hydrophobic	false
C4R	CG2	ILE- 213	4.46	0	Hydrophobic	false
C2'	CD1	ILE- 213	3.28	0	Hydrophobic	false
O2B	N	PHE- 214	3.18	155.03	H-Bond (Protein Donor)	false
C4R	CB	PHE- 214	4.35	0	Hydrophobic	false