scPDB - 1y4l entry

Protein Data Bank Entry:

PDB ID : 1y4l

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2004-12-01

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 2
ID:	PA2H2_BOTAS
AC:	P24605
Organism:	Bothrops asper
Reign:	Eukaryota
TaxID:	8722
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	52 %
B	48 %

Ligand binding site composition:

B-Factor:	25.921
Number of residues:	54
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.644	1083.375

% Hydrophobic	% Polar
57.94	42.06
According to VolSite

Ligand :

HET Code:	SVR
Formula:	C51H34N6O23S6
Molecular weight:	1291.232 g/mol
DrugBank ID:	DB04786
Buried Surface Area:	50.06 %
Polar Surface area:	551 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	6
Rings:	8
Aromatic rings:	8
Anionic atoms:	6
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
8.77034	3.58705	8.09571

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
C27	CG	LEU- 2	3.45	0	Hydrophobic	false
C59	CD2	LEU- 2	4.26	0	Hydrophobic	false
C52	CD2	LEU- 2	3.49	0	Hydrophobic	false
C33	CD2	LEU- 2	3.64	0	Hydrophobic	false
C59	CD2	LEU- 5	3.35	0	Hydrophobic	false
C37	CB	VAL- 31	4.49	0	Hydrophobic	false
C39	CG1	VAL- 31	4.2	0	Hydrophobic	false
C47	CB	VAL- 31	3.76	0	Hydrophobic	false
C48	CG1	VAL- 31	3.49	0	Hydrophobic	false
C18	CD2	LEU- 32	4.48	0	Hydrophobic	false
O29	N	ARG- 34	2.97	175.86	H-Bond (Protein Donor)	false
O30	NE	ARG- 34	2.53	165.36	H-Bond (Protein Donor)	false
O30	NH2	ARG- 34	3.33	125.29	H-Bond (Protein Donor)	false
O82	NH1	ARG- 34	3.06	139.8	H-Bond (Protein Donor)	false
O30	CZ	ARG- 34	3.36	0	Ionic (Protein Cationic)	false
O82	CZ	ARG- 34	3.99	0	Ionic (Protein Cationic)	false
C71	CD	ARG- 34	3.93	0	Hydrophobic	false
C12	CG	ARG- 34	3.96	0	Hydrophobic	false
C70	CD	ARG- 34	3.43	0	Hydrophobic	false
C62	CB	LYS- 49	3.68	0	Hydrophobic	false
C7	CB	LYS- 49	3.52	0	Hydrophobic	false
C58	CG	LYS- 49	3.24	0	Hydrophobic	false
C60	CG	LYS- 49	3.61	0	Hydrophobic	false
C67	CB	LYS- 49	3.59	0	Hydrophobic	false
C27	CE2	TYR- 52	4.45	0	Hydrophobic	false
C59	CE2	TYR- 52	3.63	0	Hydrophobic	false
C9	CD2	TYR- 52	3.45	0	Hydrophobic	false
C60	CD2	TYR- 52	2.78	0	Hydrophobic	false
C62	CB	TYR- 52	3.57	0	Hydrophobic	false
O28	NZ	LYS- 53	3	168.7	H-Bond (Protein Donor)	false
O30	NZ	LYS- 53	3.15	126.49	H-Bond (Protein Donor)	false
O80	NZ	LYS- 53	2.64	147.63	H-Bond (Protein Donor)	false
O28	NZ	LYS- 53	3	0	Ionic (Protein Cationic)	false
O30	NZ	LYS- 53	3.15	0	Ionic (Protein Cationic)	false
O80	NZ	LYS- 53	2.64	0	Ionic (Protein Cationic)	false
O82	NZ	LYS- 53	3.34	0	Ionic (Protein Cationic)	false
C67	CG	LYS- 53	4.14	0	Hydrophobic	false
C70	CD	LYS- 53	3.83	0	Hydrophobic	false
C14	CB	PRO- 68	3.62	0	Hydrophobic	false
C27	CG	LYS- 69	3.55	0	Hydrophobic	false
C14	CB	LYS- 69	3.66	0	Hydrophobic	false
O79	NZ	LYS- 69	3.79	0	Ionic (Protein Cationic)	false
O34	NZ	LYS- 70	3.69	0	Ionic (Protein Cationic)	false
O25	NZ	LYS- 70	3.99	0	Ionic (Protein Cationic)	false
O86	NZ	LYS- 70	3.38	0	Ionic (Protein Cationic)	false
C18	CD	LYS- 70	4.42	0	Hydrophobic	false
O86	NZ	LYS- 70	3.38	132.12	H-Bond (Protein Donor)	false