scPDB - 3otw entry

Protein Data Bank Entry:

PDB ID : 3otw

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2010-09-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphopantetheine adenylyltransferase
ID:	COAD_HELPY
AC:	O26010
Organism:	Helicobacter pylori
Reign:	Bacteria
TaxID:	85962
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	8 %
F	92 %

Ligand binding site composition:

B-Factor:	32.213
Number of residues:	53
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.006	769.500

% Hydrophobic	% Polar
46.05	53.95
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	62.21 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
-23.0297	-28.9196	-9.61198

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
CDP	CB	PRO- 8	3.78	0	Hydrophobic	false
O4A	N	THR- 10	2.98	169.92	H-Bond (Protein Donor)	false
O5A	OG1	THR- 10	2.79	160.06	H-Bond (Protein Donor)	false
O2B	NE2	HIS- 18	3.2	140.02	H-Bond (Protein Donor)	false
DuAr	DuAr	HIS- 18	3.6	0	Aromatic Face/Face	false
CEP	CB	ALA- 37	3.53	0	Hydrophobic	false
O1A	NZ	LYS- 42	2.88	162.41	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 42	2.88	0	Ionic (Protein Cationic)	false
O5A	NZ	LYS- 42	3.52	0	Ionic (Protein Cationic)	false
O5P	N	LEU- 74	2.82	161.72	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 88	2.86	128.43	H-Bond (Protein Donor)	false
O3A	NH2	ARG- 88	3.49	164.03	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 91	3.85	25.35	Pi/Cation	false
O2A	OH	TYR- 98	2.81	141.53	H-Bond (Protein Donor)	false
CAP	SD	MET- 102	4.41	0	Hydrophobic	false
S1P	CG	MET- 102	3.99	0	Hydrophobic	false
S1P	CB	ALA- 105	3.83	0	Hydrophobic	false
N3A	N	SER- 129	3.37	137.28	H-Bond (Protein Donor)	false
C1B	CB	SER- 129	4.27	0	Hydrophobic	false
O7A	CZ	ARG- 133	3.7	0	Ionic (Protein Cationic)	false
O9A	CZ	ARG- 133	3.33	0	Ionic (Protein Cationic)	false
O7A	NH1	ARG- 133	2.99	122.78	H-Bond (Protein Donor)	false
O9A	NH1	ARG- 133	3.14	132.47	H-Bond (Protein Donor)	false
O9A	NH2	ARG- 133	2.66	161.14	H-Bond (Protein Donor)	false
O5P	O	HOH- 164	2.75	154.81	H-Bond (Protein Donor)	false