scPDB - 4x3q entry

Protein Data Bank Entry:

PDB ID : 4x3q

Resolution :2.590 Å

Experimental Method : X-ray

Deposition Date : 2014-12-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	SibL
ID:	C0LTM6_9ACTN
AC:	C0LTM6
Organism:	Streptosporangium sibiricum
Reign:	Bacteria
TaxID:	457432
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	44.148
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.350	459.000

% Hydrophobic	% Polar
49.26	50.74
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	75.33 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
0.394154	9.40688	2.44412

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
C4'	CE1	TYR- 134	4.42	0	Hydrophobic	false
C5'	CE1	TYR- 134	3.66	0	Hydrophobic	false
C2'	CD1	TYR- 134	3.59	0	Hydrophobic	false
C3'	CZ	TYR- 148	4.23	0	Hydrophobic	false
O3'	OH	TYR- 148	2.59	161.73	H-Bond (Protein Donor)	false
SD	CE	MET- 151	3.92	0	Hydrophobic	false
CG	CE	MET- 151	3.6	0	Hydrophobic	false
O	OG	SER- 155	3.07	145.82	H-Bond (Protein Donor)	false
N	O	GLY- 178	2.81	153.39	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 201	2.85	167.5	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 201	3.36	127.95	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 201	2.57	146.41	H-Bond (Ligand Donor)	false
C2'	CD	ARG- 202	4.18	0	Hydrophobic	false
O2'	NH1	ARG- 202	2.57	164.47	H-Bond (Protein Donor)	false
N6	OD2	ASP- 228	3.12	153.92	H-Bond (Ligand Donor)	false
N1	N	ILE- 229	3.16	159.05	H-Bond (Protein Donor)	false
N	O	ALA- 244	3.12	157	H-Bond (Ligand Donor)	false
CG	CB	HIS- 245	4.1	0	Hydrophobic	false
O4'	NE2	GLN- 246	3.03	168.97	H-Bond (Protein Donor)	false
C5'	CD1	ILE- 249	3.69	0	Hydrophobic	false