scPDB - 3kkz entry

Protein Data Bank Entry:

PDB ID : 3kkz

Resolution :1.680 Å

Experimental Method : X-ray

Deposition Date : 2009-11-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	Q5LES9_BACFN
AC:	Q5LES9
Organism:	Bacteroides fragilis
Reign:	Bacteria
TaxID:	272559
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.000
Number of residues:	38
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.995	880.875

% Hydrophobic	% Polar
44.44	55.56
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	69.75 %
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
-1.42089	76.4945	16.2636

Binding mode :

What is Poseview ?

2D View
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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
O	NE	ARG- 25	3.5	130.71	H-Bond (Protein Donor)	false
O	NH2	ARG- 25	2.75	165.42	H-Bond (Protein Donor)	false
OXT	NE	ARG- 25	2.98	174.64	H-Bond (Protein Donor)	false
O	CZ	ARG- 25	3.56	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 25	3.84	0	Ionic (Protein Cationic)	false
OXT	N	GLN- 26	3.02	166.58	H-Bond (Protein Donor)	false
CG	CB	GLN- 26	3.98	0	Hydrophobic	false
SD	CB	GLN- 26	3.97	0	Hydrophobic	false
N	O	GLY- 54	2.83	164.23	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 76	3.41	120.28	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 76	2.61	165.72	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 76	2.65	154.42	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 76	3.47	148.29	H-Bond (Ligand Donor)	false
N3	N	PHE- 77	3.22	134.47	H-Bond (Protein Donor)	false
C3'	CE2	PHE- 81	3.82	0	Hydrophobic	false
N6	OG	SER- 104	3.05	149.02	H-Bond (Ligand Donor)	false
N1	N	MET- 105	2.76	153.99	H-Bond (Protein Donor)	false
N	O	GLU- 121	2.71	164.96	H-Bond (Ligand Donor)	false
C5'	CB	ALA- 123	4.23	0	Hydrophobic	false