scPDB - 1ykd entry

Protein Data Bank Entry:

PDB ID : 1ykd

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2005-01-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenylate cyclase
ID:	P94182_9NOST
AC:	P94182
Organism:	Anabaena sp
Reign:	Bacteria
TaxID:	1167
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.722
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.443	600.750

% Hydrophobic	% Polar
65.17	34.83
According to VolSite

Ligand :

HET Code:	CMP
Formula:	C10H11N5O6P
Molecular weight:	328.198 g/mol
DrugBank ID:	DB02527
Buried Surface Area:	64.05 %
Polar Surface area:	167.48 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
4.19532	28.8285	36.8347

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
N1	NH1	ARG- 103	3.2	161.16	H-Bond (Protein Donor)	false
N7	OG1	THR- 105	2.81	158.89	H-Bond (Protein Donor)	false
N6	OG1	THR- 105	2.86	168.45	H-Bond (Ligand Donor)	false
C5'	CD1	ILE- 133	4.43	0	Hydrophobic	false
O2P	N	ILE- 139	2.98	160.86	H-Bond (Protein Donor)	false
O1P	N	ALA- 140	3.05	157.52	H-Bond (Protein Donor)	false
C5'	CE2	PHE- 164	4.1	0	Hydrophobic	false
C4'	CB	ALA- 165	4.25	0	Hydrophobic	false
O2'	OG1	THR- 176	2.96	166.92	H-Bond (Ligand Donor)	false
C3'	CE	MET- 179	4.37	0	Hydrophobic	false
O1P	NE2	GLN- 196	2.88	170.71	H-Bond (Protein Donor)	false
C2'	CD1	LEU- 198	4.02	0	Hydrophobic	false
O2P	O	HOH- 516	2.65	146.49	H-Bond (Protein Donor)	false