scPDB - 1ro9 entry

Protein Data Bank Entry:

PDB ID : 1ro9

Resolution :2.130 Å

Experimental Method : X-ray

Deposition Date : 2003-12-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	cAMP-specific 3',5'-cyclic phosphodiesterase 4B
ID:	PDE4B_HUMAN
AC:	Q07343
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.1.4.53

Chains:

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

Ligand binding site composition:

B-Factor:	34.792
Number of residues:	32
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	ZN ZN

Cavity properties

Ligandability	Volume (Å3)
0.981	695.250

% Hydrophobic	% Polar
59.22	40.78
According to VolSite

Ligand :

HET Code:	8BR
Formula:	C10H11BrN5O7P
Molecular weight:	424.101 g/mol
DrugBank ID:	DB03349
Buried Surface Area:	61.35 %
Polar Surface area:	201.54 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
19.5581	110.712	29.4985

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
O2P	NE2	HIS- 234	3.14	134.99	H-Bond (Protein Donor)	false
O3P	NE2	HIS- 234	2.96	138.64	H-Bond (Protein Donor)	false
O5'	NE2	HIS- 234	3.5	155.22	H-Bond (Protein Donor)	false
C5'	CG	MET- 347	3.69	0	Hydrophobic	false
N1	ND2	ASN- 395	2.89	138.34	H-Bond (Protein Donor)	false
C2'	CG2	ILE- 410	4.47	0	Hydrophobic	false
BR8	CE2	PHE- 414	3.82	0	Hydrophobic	false
C2'	CZ	PHE- 414	3.45	0	Hydrophobic	false
BR8	SD	MET- 431	4.41	0	Hydrophobic	false
N7	NE2	GLN- 443	3.17	151.54	H-Bond (Protein Donor)	false
N6	OE1	GLN- 443	2.8	154.5	H-Bond (Ligand Donor)	false
C1'	CE1	PHE- 446	3.96	0	Hydrophobic	false
BR8	CG	PHE- 446	4.07	0	Hydrophobic	false