scPDB - 3ipk entry

Protein Data Bank Entry:

PDB ID : 3ipk

Resolution :2.040 Å

Experimental Method : X-ray

Deposition Date : 2009-08-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Surface protein adhesin
ID:	C9E3B4_STRMG
AC:	C9E3B4
Organism:	Streptococcus mutans
Reign:	Bacteria
TaxID:	1309
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.909
Number of residues:	21
Including
Standard Amino Acids:	18
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.431	452.250

% Hydrophobic	% Polar
35.07	64.93
According to VolSite

Ligand :

HET Code:	PMS
Formula:	C7H7O3S
Molecular weight:	171.194 g/mol
DrugBank ID:	DB03297
Buried Surface Area:	43.32 %
Polar Surface area:	65.58 Å2

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

Mass center Coordinates

X	Y	Z
6.5022	40.2103	23.0435

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
C2	CB	SER- 697	4.41	0	Hydrophobic	false
C	CZ3	TRP- 816	4.19	0	Hydrophobic	false
O3S	NH2	ARG- 824	3.47	154.62	H-Bond (Protein Donor)	false
O2S	NH1	ARG- 824	2.74	156.06	H-Bond (Protein Donor)	false
O2S	NH2	ARG- 824	3.08	136.35	H-Bond (Protein Donor)	false
O1S	NH2	ARG- 824	3.1	141.89	H-Bond (Protein Donor)	false
O2S	CZ	ARG- 824	3.34	0	Ionic (Protein Cationic)	false