scPDB - 1wc5 entry

Protein Data Bank Entry:

PDB ID : 1wc5

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2004-11-08

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:	O32393_ARTPT
AC:	O32393
Organism:	Arthrospira platensis
Reign:	Bacteria
TaxID:	118562
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	49 %
C	51 %

Ligand binding site composition:

B-Factor:	28.955
Number of residues:	36
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	3
Water Molecules:	1
Cofactors:
Metals:	MG CA

Cavity properties

Ligandability	Volume (Å3)
0.298	2365.875

% Hydrophobic	% Polar
40.94	59.06
According to VolSite

Ligand :

HET Code:	APC
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB02596
Buried Surface Area:	57.33 %
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
-3.11077	1.69594	5.35826

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
O3G	N	GLY- 1020	2.53	165.87	H-Bond (Protein Donor)	false
O2B	N	PHE- 1021	2.85	154.29	H-Bond (Protein Donor)	false
O1B	N	THR- 1022	3.16	143.99	H-Bond (Protein Donor)	false
C3A	CB	THR- 1022	4.04	0	Hydrophobic	false
N1	NZ	LYS- 1057	2.94	155.81	H-Bond (Protein Donor)	false
O1G	NH2	ARG- 1117	3.3	125.23	H-Bond (Protein Donor)	false
O2G	NH1	ARG- 1117	3.49	156.99	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 1117	2.92	168.28	H-Bond (Protein Donor)	false
O3G	CZ	ARG- 1117	3.83	0	Ionic (Protein Cationic)	false
N6	OG1	THR- 1139	3.35	162.18	H-Bond (Ligand Donor)	false
C5'	CB	ASN- 1146	4.23	0	Hydrophobic	false
C4'	CB	ALA- 1149	4.15	0	Hydrophobic	false
C1'	CB	ALA- 1149	4.14	0	Hydrophobic	false
O2G	MG	MG- 2000	2.68	0	Metal Acceptor	false
O2A	MG	MG- 2000	2.73	0	Metal Acceptor	false
N7	O	HOH- 2019	3.07	179.98	H-Bond (Protein Donor)	false
O2G	CA	CA- 2100	2.43	0	Metal Acceptor	false
O2B	CA	CA- 2100	2.34	0	Metal Acceptor	false
O1A	CA	CA- 2100	2.62	0	Metal Acceptor	false