scPDB - 4ib4 entry

Protein Data Bank Entry:

PDB ID : 4ib4

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2012-12-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.660	8.660	8.660	0.000	8.660	1

List of CHEMBLId :

CHEMBL442

Binding Site :

Uniprot Annotation

Name:	5-hydroxytryptamine receptor 2B
ID:	5HT2B_HUMAN
AC:	P41595
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	57.973
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.524	1005.750

% Hydrophobic	% Polar
59.40	40.60
According to VolSite

Ligand :

HET Code:	ERM
Formula:	C33H36N5O5
Molecular weight:	582.669 g/mol
DrugBank ID:	DB00696
Buried Surface Area:	68.73 %
Polar Surface area:	119.41 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	8
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
22.4478	18.2838	11.7261

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
C26	CH2	TRP- 131	4.19	0	Hydrophobic	false
C26	CD2	LEU- 132	3.77	0	Hydrophobic	false
N2	OD1	ASP- 135	2.63	169.6	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 135	2.63	0	Ionic (Ligand Cationic)	false
C9	CG2	VAL- 136	3.94	0	Hydrophobic	false
C13	CG1	VAL- 136	3.63	0	Hydrophobic	false
C3	CB	SER- 139	3.43	0	Hydrophobic	false
C26	CG2	VAL- 208	4.2	0	Hydrophobic	false
C29	CB	LEU- 209	4.16	0	Hydrophobic	false
O3	N	LEU- 209	2.88	166.29	H-Bond (Protein Donor)	false
C31	CB	LYS- 211	3.96	0	Hydrophobic	false
C27	SD	MET- 218	4.37	0	Hydrophobic	false
C29	CE	MET- 218	3.67	0	Hydrophobic	false
C10	SD	MET- 218	3.7	0	Hydrophobic	false
C32	CG	MET- 218	3.69	0	Hydrophobic	false
C13	CB	ALA- 225	4.26	0	Hydrophobic	false
C3	CH2	TRP- 337	4.46	0	Hydrophobic	false
C6	CZ	PHE- 340	4.35	0	Hydrophobic	false
C32	CD2	LEU- 347	3.67	0	Hydrophobic	false
C32	CG2	VAL- 348	3.75	0	Hydrophobic	false
C22	CB	GLN- 359	4.32	0	Hydrophobic	false
C23	CB	LEU- 362	4.13	0	Hydrophobic	false
C33	CD1	LEU- 362	3.77	0	Hydrophobic	false
C22	CB	GLU- 363	4.23	0	Hydrophobic	false