scPDB - 2vkd entry

Protein Data Bank Entry:

PDB ID : 2vkd

Resolution :2.530 Å

Experimental Method : X-ray

Deposition Date : 2007-12-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cytotoxin L
ID:	Q46342_CLOSO
AC:	Q46342
Organism:	Clostridium sordellii
Reign:	Bacteria
TaxID:	1505
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	24.971
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.202	563.625

% Hydrophobic	% Polar
46.71	53.29
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	78.32 %
Polar Surface area:	316.82 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
36.4164	-9.55539	69.2785

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
O2C	O	ILE- 101	2.75	174.72	H-Bond (Ligand Donor)	false
C3C	CZ3	TRP- 102	4.34	0	Hydrophobic	false
C2C	CE3	TRP- 102	3.75	0	Hydrophobic	false
N3	O	ILE- 103	2.89	161.26	H-Bond (Ligand Donor)	false
O2	N	ILE- 103	3	155.98	H-Bond (Protein Donor)	false
O4	ND2	ASN- 139	2.9	172.62	H-Bond (Protein Donor)	false
C1C	CB	SER- 269	3.81	0	Hydrophobic	false
O2C	OG	SER- 269	3.15	155.08	H-Bond (Protein Donor)	false
O4'	OD1	ASP- 270	2.85	151.38	H-Bond (Ligand Donor)	false
O6'	OD1	ASP- 270	3.37	127.97	H-Bond (Ligand Donor)	false
O3'	NH1	ARG- 273	2.75	159.14	H-Bond (Protein Donor)	false
O3C	OD1	ASP- 286	3.01	127.16	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 286	2.6	164.85	H-Bond (Ligand Donor)	false
C3C	CG2	VAL- 287	4.46	0	Hydrophobic	false
O3C	N	VAL- 287	3.23	149.85	H-Bond (Protein Donor)	false
C2'	CG1	ILE- 383	4.36	0	Hydrophobic	false
C2'	CB	GLN- 385	4.44	0	Hydrophobic	false
C6'	CD1	ILE- 466	3.93	0	Hydrophobic	false
O3A	OG	SER- 518	3.41	138.27	H-Bond (Protein Donor)	false
O2B	OG	SER- 518	2.5	148.63	H-Bond (Protein Donor)	false
O2A	N	LEU- 519	2.81	143.96	H-Bond (Protein Donor)	false
O2B	NE1	TRP- 520	3.29	121.63	H-Bond (Protein Donor)	false
O5'	NE1	TRP- 520	3.4	123.13	H-Bond (Protein Donor)	false
C5'	CE2	TRP- 520	4.28	0	Hydrophobic	false
O1A	MN	MN- 1541	2.09	0	Metal Acceptor	false
O1B	MN	MN- 1541	1.98	0	Metal Acceptor	false