scPDB - 3cyl entry

Protein Data Bank Entry:

PDB ID : 3cyl

Resolution :1.870 Å

Experimental Method : X-ray

Deposition Date : 2008-04-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Basic phospholipase A2 homolog piratoxin-2
ID:	PA2H2_BOTPI
AC:	P82287
Organism:	Bothrops pirajai
Reign:	Eukaryota
TaxID:	113192
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	82 %
B	18 %

Ligand binding site composition:

B-Factor:	22.545
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.239	2524.500

% Hydrophobic	% Polar
54.41	45.59
According to VolSite

Ligand :

HET Code:	VIT
Formula:	C29H50O2
Molecular weight:	430.706 g/mol
DrugBank ID:	-
Buried Surface Area:	39.66 %
Polar Surface area:	29.46 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	1
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
5.88958	-2.39132	4.58652

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
C13	CD1	LEU- 2	4.08	0	Hydrophobic	false
C3	CD1	LEU- 2	4.09	0	Hydrophobic	false
C4	CD1	LEU- 2	3.75	0	Hydrophobic	false
C19	CD1	LEU- 2	3.57	0	Hydrophobic	false
C15	CD1	LEU- 2	3.57	0	Hydrophobic	false
C15	CD2	LEU- 5	4.1	0	Hydrophobic	false
C19	CB	LEU- 5	4.15	0	Hydrophobic	false
C11	CD2	LEU- 5	4.05	0	Hydrophobic	false
C28	CD	LYS- 7	4.04	0	Hydrophobic	false
C26	CB	LYS- 7	3.95	0	Hydrophobic	false
C16	CD1	ILE- 9	4.48	0	Hydrophobic	false
C29	CD2	LEU- 10	4.37	0	Hydrophobic	false
C25	CD2	LEU- 10	3.77	0	Hydrophobic	false
C17	CB	PRO- 18	3.82	0	Hydrophobic	false
C23	CG	PRO- 18	3.41	0	Hydrophobic	false
C22	CG	PRO- 18	3.89	0	Hydrophobic	false
C6	CG1	VAL- 31	3.6	0	Hydrophobic	false
C12	CG1	VAL- 31	3.31	0	Hydrophobic	false
C8	CE2	TYR- 52	4.12	0	Hydrophobic	false
O2	NZ	LYS- 69	3.49	155.49	H-Bond (Protein Donor)	false