scPDB - 1cbq entry

Protein Data Bank Entry:

PDB ID : 1cbq

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1994-09-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cellular retinoic acid-binding protein 2
ID:	RABP2_HUMAN
AC:	P29373
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:	22.663
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.391	681.750

% Hydrophobic	% Polar
54.46	45.54
According to VolSite

Ligand :

HET Code:	RE9
Formula:	C20H27O2
Molecular weight:	299.427 g/mol
DrugBank ID:	DB08467
Buried Surface Area:	64.42 %
Polar Surface area:	40.12 Å2

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

Mass center Coordinates

X	Y	Z
68.4356	38.6955	34.6757

Binding mode :

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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
C10	CZ	PHE- 15	4.11	0	Hydrophobic	false
C20	CE1	PHE- 15	3.99	0	Hydrophobic	false
C16	CD1	LEU- 19	4.44	0	Hydrophobic	false
C16	CG2	VAL- 24	4.44	0	Hydrophobic	false
C2	CB	LEU- 28	4.11	0	Hydrophobic	false
C4	CG2	ILE- 31	4.39	0	Hydrophobic	false
C4	CB	ALA- 32	4.27	0	Hydrophobic	false
C16	CB	ALA- 32	4.04	0	Hydrophobic	false
C10	CB	ALA- 32	4.09	0	Hydrophobic	false
C10	CB	ALA- 36	3.98	0	Hydrophobic	false
C4	CD	ARG- 59	4.46	0	Hydrophobic	false
C17	CD	ARG- 59	4.18	0	Hydrophobic	false
C19	CG	ARG- 59	4.01	0	Hydrophobic	false
C20	CG1	VAL- 76	4.26	0	Hydrophobic	false
C20	CE	MET- 123	4.26	0	Hydrophobic	false
O2	NE	ARG- 132	3.22	132.81	H-Bond (Protein Donor)	false
O2	NH2	ARG- 132	2.75	155.55	H-Bond (Protein Donor)	false
O2	CZ	ARG- 132	3.41	0	Ionic (Protein Cationic)	false
O2	OH	TYR- 134	2.65	169.11	H-Bond (Protein Donor)	false
O1	O	HOH- 332	2.99	179.98	H-Bond (Protein Donor)	false