scPDB - 3n0y entry

Protein Data Bank Entry:

PDB ID : 3n0y

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2010-05-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenylate cyclase 2
ID:	Q7CH76_YERPE
AC:	Q7CH76
Organism:	Yersinia pestis
Reign:	Bacteria
TaxID:	632
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.215
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.259	519.750

% Hydrophobic	% Polar
49.35	50.65
According to VolSite

Ligand :

HET Code:	APC
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB02596
Buried Surface Area:	64.04 %
Polar Surface area:	310.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-4.31781	2.23419	14.4601

Binding mode :

What is Poseview ?

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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
C2'	CD2	PHE- 5	3.77	0	Hydrophobic	false
O1G	NZ	LYS- 14	2.86	156.52	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 14	2.86	0	Ionic (Protein Cationic)	false
O2A	NH1	ARG- 63	2.76	147.15	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 63	3.26	129.26	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 63	3.43	0	Ionic (Protein Cationic)	false
C5'	CD1	ILE- 74	3.91	0	Hydrophobic	false
C4'	CG2	ILE- 74	4.48	0	Hydrophobic	false
O2G	NZ	LYS- 76	3.42	0	Ionic (Protein Cationic)	false
C3A	CD	LYS- 76	4.08	0	Hydrophobic	false
C4'	SG	CYS- 83	3.62	0	Hydrophobic	false
C1'	CB	ALA- 85	4.02	0	Hydrophobic	false
O2B	NZ	LYS- 111	2.96	148.33	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 111	2.96	0	Ionic (Protein Cationic)	false
O1B	NH1	ARG- 113	2.93	172.48	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 113	2.73	149.15	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 113	3.85	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 113	3.81	0	Ionic (Protein Cationic)	false
O1G	N	TYR- 173	3.46	150.79	H-Bond (Protein Donor)	false
O3G	N	TYR- 173	2.54	138.69	H-Bond (Protein Donor)	false
O1B	MN	MN- 182	2.1	0	Metal Acceptor	false
O1A	MN	MN- 182	2.28	0	Metal Acceptor	false