scPDB - 4k39 entry

Protein Data Bank Entry:

PDB ID : 4k39

Resolution :1.780 Å

Experimental Method : X-ray

Deposition Date : 2013-04-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Anaerobic sulfatase-maturating enzyme
ID:	ANSME_CLOP1
AC:	Q0TTH1
Organism:	Clostridium perfringens
Reign:	Bacteria
TaxID:	195103
EC Number:	1.8.98

Chains:

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

Ligand binding site composition:

B-Factor:	22.608
Number of residues:	40
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.742	1792.125

% Hydrophobic	% Polar
36.16	63.84
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	72.94 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
23.0745	24.2926	43.7262

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
N6	O	TYR- 21	3.31	153.6	H-Bond (Ligand Donor)	false
CE	SG	CYS- 22	4.19	0	Hydrophobic	false
CE	CD1	TYR- 24	3.77	0	Hydrophobic	false
N	O	GLY- 66	2.85	154.18	H-Bond (Ligand Donor)	false
N	OE1	GLU- 67	3.3	138.26	H-Bond (Ligand Donor)	false
OXT	NE2	GLN- 98	2.69	165.3	H-Bond (Protein Donor)	false
CB	CG	GLN- 98	3.56	0	Hydrophobic	false
C5'	CG	GLN- 98	4.01	0	Hydrophobic	false
O	OG	SER- 122	3.19	164.48	H-Bond (Protein Donor)	false
OXT	OG	SER- 122	2.54	130.24	H-Bond (Protein Donor)	false
C3'	CB	SER- 122	4.44	0	Hydrophobic	false
O3'	OG	SER- 122	2.87	156.14	H-Bond (Ligand Donor)	false
O	NH2	ARG- 134	2.98	143.08	H-Bond (Protein Donor)	false
O2'	NH1	ARG- 134	3.04	124.97	H-Bond (Protein Donor)	false
C4'	CD2	LEU- 163	3.95	0	Hydrophobic	false
C1'	CG2	VAL- 165	3.9	0	Hydrophobic	false
C4'	CD1	ILE- 192	4.45	0	Hydrophobic	false
C1'	CD1	ILE- 192	4.33	0	Hydrophobic	false
N6	O	LEU- 195	2.88	158.26	H-Bond (Ligand Donor)	false
N1	N	LEU- 195	2.81	169.92	H-Bond (Protein Donor)	false
O2'	O	HOH- 605	3.12	130.86	H-Bond (Ligand Donor)	false