scPDB - 3hmv entry

Protein Data Bank Entry:

PDB ID : 3hmv

Resolution :2.230 Å

Experimental Method : X-ray

Deposition Date : 2009-05-29

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
A	100 %

Ligand binding site composition:

B-Factor:	33.371
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	ZN MG

Cavity properties

Ligandability	Volume (Å3)
1.155	762.750

% Hydrophobic	% Polar
50.88	49.12
According to VolSite

Ligand :

HET Code:	HBT
Formula:	C17H17N3O4S
Molecular weight:	359.400 g/mol
DrugBank ID:	-
Buried Surface Area:	67.09 %
Polar Surface area:	146.25 Å2

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

Mass center Coordinates

X	Y	Z
-12.9881	-28.0422	-5.9898

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
O4	O	HOH- 23	2.78	164.75	H-Bond (Protein Donor)	false
C10	CG	MET- 347	3.51	0	Hydrophobic	false
C9	CD2	LEU- 393	3.63	0	Hydrophobic	false
N3	OD1	ASN- 395	2.95	160.86	H-Bond (Ligand Donor)	false
C2	CZ	TYR- 403	4.25	0	Hydrophobic	false
C17	CE1	TYR- 403	3.99	0	Hydrophobic	false
C2	CG2	THR- 407	4.4	0	Hydrophobic	false
C17	CG2	ILE- 410	3.71	0	Hydrophobic	false
C3	CG2	ILE- 410	4.27	0	Hydrophobic	false
C3	SD	MET- 411	3.9	0	Hydrophobic	false
C4	CE2	PHE- 414	4.24	0	Hydrophobic	false
S1	CE	MET- 431	4.43	0	Hydrophobic	false
C4	SD	MET- 431	3.9	0	Hydrophobic	false
C1	SD	MET- 431	4.43	0	Hydrophobic	false
C1	CB	SER- 442	3.78	0	Hydrophobic	false
C1	CG	GLN- 443	4.26	0	Hydrophobic	false
C4	CD2	PHE- 446	4.16	0	Hydrophobic	false
C2	CD2	PHE- 446	4.22	0	Hydrophobic	false
C17	CE2	PHE- 446	4.04	0	Hydrophobic	false
DuAr	DuAr	PHE- 446	3.92	0	Aromatic Face/Face	false