scPDB - 1kvo entry

Protein Data Bank Entry:

PDB ID : 1kvo

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1996-07-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phospholipase A2, membrane associated
ID:	PA2GA_HUMAN
AC:	P14555
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.090
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
1.002	1562.625

% Hydrophobic	% Polar
45.79	54.21
According to VolSite

Ligand :

HET Code:	OAP
Formula:	C31H36NO3S
Molecular weight:	502.687 g/mol
DrugBank ID:	-
Buried Surface Area:	64.39 %
Polar Surface area:	94.53 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
-56.7336	79.5175	59.823

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
S11	CD2	LEU- 2	3.67	0	Hydrophobic	false
C12	CD1	LEU- 2	4.06	0	Hydrophobic	false
C52	CB	LEU- 2	4.11	0	Hydrophobic	false
S11	CE2	PHE- 5	4.38	0	Hydrophobic	false
C53	CB	PHE- 5	4.23	0	Hydrophobic	false
C25	CE2	PHE- 5	3.91	0	Hydrophobic	false
C53	CB	HIS- 6	3.74	0	Hydrophobic	false
C54	CD1	ILE- 9	3.78	0	Hydrophobic	false
C28	CB	ALA- 17	3.79	0	Hydrophobic	false
C41	CB	ALA- 18	3.77	0	Hydrophobic	false
C51	CB	ALA- 18	4.34	0	Hydrophobic	false
C27	CB	TYR- 21	4.06	0	Hydrophobic	false
C24	CB	CYS- 28	4.48	0	Hydrophobic	false
O21	N	GLY- 29	2.82	146.6	H-Bond (Protein Donor)	false
C17	CG2	VAL- 30	3.66	0	Hydrophobic	false
O31	N	GLY- 31	3.11	169.37	H-Bond (Protein Donor)	false
O32	N	GLY- 31	3	123.4	H-Bond (Protein Donor)	false
C22	SG	CYS- 44	3.67	0	Hydrophobic	false
N21	ND1	HIS- 47	2.96	167.39	H-Bond (Ligand Donor)	false
C22	CB	HIS- 47	3.88	0	Hydrophobic	false
C3	CB	ASP- 48	4.49	0	Hydrophobic	false
C1	CE2	TYR- 51	3.57	0	Hydrophobic	false
C3	CD2	TYR- 51	4.03	0	Hydrophobic	false
C23	CZ	PHE- 98	4.29	0	Hydrophobic	false
C25	CE2	PHE- 98	4.08	0	Hydrophobic	false
O32	CA	CA- 191	2.37	0	Metal Acceptor	false
O21	CA	CA- 191	2.61	0	Metal Acceptor	false