scPDB - 2y30 entry

Protein Data Bank Entry:

PDB ID : 2y30

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2010-12-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative repressor SimReg2
ID:	Q9AMH9_STRAT
AC:	Q9AMH9
Organism:	Streptomyces antibioticus
Reign:	Bacteria
TaxID:	1890
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	58 %
B	42 %

Ligand binding site composition:

B-Factor:	19.885
Number of residues:	53
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.641	1083.375

% Hydrophobic	% Polar
63.24	36.76
According to VolSite

Ligand :

HET Code:	SM8
Formula:	C46H41ClNO18
Molecular weight:	931.267 g/mol
DrugBank ID:	-
Buried Surface Area:	54.22 %
Polar Surface area:	308.34 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	7
Rings:	8
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
30.4195	25.4721	-22.1657

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
CL4	CG2	ILE- 83	3.43	0	Hydrophobic	false
C4F	CG2	THR- 86	4.39	0	Hydrophobic	false
C4E	CD1	LEU- 88	4.02	0	Hydrophobic	false
C4D	CB	ALA- 103	4.21	0	Hydrophobic	false
C4E	CB	GLU- 106	4.45	0	Hydrophobic	false
C4C	CD	LYS- 107	3.84	0	Hydrophobic	false
C4D	CB	LYS- 107	3.54	0	Hydrophobic	false
C2F	CG	PRO- 126	4.44	0	Hydrophobic	false
C2B	CZ2	TRP- 128	4.33	0	Hydrophobic	false
C4F	CB	GLN- 135	4.29	0	Hydrophobic	false
C4G	CB	GLN- 135	3.92	0	Hydrophobic	false
C4C	CG2	VAL- 139	4.2	0	Hydrophobic	false
C3D	CD2	LEU- 154	3.28	0	Hydrophobic	false
O4A	OH	TYR- 160	2.92	161.34	H-Bond (Protein Donor)	false
C2F	CZ2	TRP- 174	3.97	0	Hydrophobic	false
C2F	CE	MET- 185	4.33	0	Hydrophobic	false
C2F	CZ3	TRP- 188	3.87	0	Hydrophobic	false
C1R	CB	MET- 189	4.32	0	Hydrophobic	false
C1S	CG	MET- 189	3.72	0	Hydrophobic	false
C1A	CE	MET- 189	3.62	0	Hydrophobic	false
C2E	CG	MET- 189	4.17	0	Hydrophobic	false
C1B	CE	MET- 189	3.5	0	Hydrophobic	false
C1K	CG2	VAL- 200	3.69	0	Hydrophobic	false
O1B	O	LEU- 212	3.05	151.63	H-Bond (Ligand Donor)	false
C1K	CD1	LEU- 212	3.98	0	Hydrophobic	false
C2B	CD2	LEU- 212	3.79	0	Hydrophobic	false
C1B	CD2	LEU- 212	3.72	0	Hydrophobic	false
C2E	CB	PRO- 218	4.5	0	Hydrophobic	false
C2C	CG	PRO- 218	4.2	0	Hydrophobic	false