scPDB - 1fbm entry

Protein Data Bank Entry:

PDB ID : 1fbm

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2000-07-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cartilage oligomeric matrix protein
ID:	COMP_RAT
AC:	P35444
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	21 %
B	24 %
C	18 %
D	24 %
E	15 %

Ligand binding site composition:

B-Factor:	25.047
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.194	411.750

% Hydrophobic	% Polar
82.79	17.21
According to VolSite

Ligand :

HET Code:	RTL
Formula:	C20H30O
Molecular weight:	286.452 g/mol
DrugBank ID:	DB00162
Buried Surface Area:	79.06 %
Polar Surface area:	20.23 Å2

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

Mass center Coordinates

X	Y	Z
32.7582	47.3653	-4.7989

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
C2	CG2	THR- 40	4.12	0	Hydrophobic	false
C16	CG2	THR- 40	3.93	0	Hydrophobic	false
C17	CG2	THR- 40	3.64	0	Hydrophobic	false
C3	CG2	THR- 40	3.8	0	Hydrophobic	false
C3	CB	THR- 40	3.99	0	Hydrophobic	false
C4	CG	LEU- 44	4.18	0	Hydrophobic	false
C4	CG	LEU- 44	3.8	0	Hydrophobic	false
C6	CG	LEU- 44	4.41	0	Hydrophobic	false
C16	CD2	LEU- 44	3.34	0	Hydrophobic	false
C17	CD2	LEU- 44	3.86	0	Hydrophobic	false
C19	CD1	LEU- 44	4.01	0	Hydrophobic	false
C19	CD2	LEU- 44	3.64	0	Hydrophobic	false
C17	CD2	LEU- 44	3.26	0	Hydrophobic	false
C6	CD1	LEU- 44	3.55	0	Hydrophobic	false
C3	CD1	LEU- 44	3.74	0	Hydrophobic	false
C16	CD1	LEU- 44	3.41	0	Hydrophobic	false
C19	CG1	VAL- 47	3.28	0	Hydrophobic	false
C19	CG1	VAL- 47	4.47	0	Hydrophobic	false
C20	CG1	VAL- 47	3.9	0	Hydrophobic	false
C13	CD1	LEU- 51	4.08	0	Hydrophobic	false
C15	CD1	LEU- 51	3.64	0	Hydrophobic	false
C15	CD2	LEU- 51	4.26	0	Hydrophobic	false
C20	CD1	LEU- 51	4.12	0	Hydrophobic	false
C13	CD1	LEU- 51	3.88	0	Hydrophobic	false
C20	CD1	LEU- 51	3.27	0	Hydrophobic	false
C14	CD1	LEU- 51	3.63	0	Hydrophobic	false
C15	CD2	LEU- 51	3.57	0	Hydrophobic	false
C14	CD2	LEU- 51	3.47	0	Hydrophobic	false
O1	NE2	GLN- 54	3.49	164.21	H-Bond (Protein Donor)	false
O1	NE2	GLN- 54	3.15	143.72	H-Bond (Protein Donor)	false