scPDB - 3fmz entry

Protein Data Bank Entry:

PDB ID : 3fmz

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2008-12-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Retinol-binding protein 4
ID:	RET4_HUMAN
AC:	P02753
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.135
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.456	597.375

% Hydrophobic	% Polar
74.01	25.99
According to VolSite

Ligand :

HET Code:	2T1
Formula:	C20H18F3N2O3
Molecular weight:	391.364 g/mol
DrugBank ID:	DB06985
Buried Surface Area:	70.55 %
Polar Surface area:	72.47 Å2

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

Mass center Coordinates

X	Y	Z
19.7077	-65.0436	15.6892

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
C19	CB	LEU- 35	3.84	0	Hydrophobic	false
O1	N	LEU- 37	3.43	138.67	H-Bond (Protein Donor)	false
F3	CB	ALA- 43	4.36	0	Hydrophobic	false
F3	CZ	PHE- 45	4.29	0	Hydrophobic	false
C5	CB	ALA- 55	4.17	0	Hydrophobic	false
C11	CB	ALA- 57	3.87	0	Hydrophobic	false
C2	CB	ALA- 57	3.76	0	Hydrophobic	false
C8	SD	MET- 73	4.49	0	Hydrophobic	false
C17	CE	MET- 73	4.01	0	Hydrophobic	false
C11	CE	MET- 73	3.79	0	Hydrophobic	false
C2	CG	MET- 73	4.09	0	Hydrophobic	false
F1	CE	MET- 88	3.66	0	Hydrophobic	false
C5	SD	MET- 88	3.79	0	Hydrophobic	false
C3	CE	MET- 88	3.99	0	Hydrophobic	false
C8	CD2	TYR- 90	3.83	0	Hydrophobic	false
C1	CB	TYR- 90	3.95	0	Hydrophobic	false
O3	OH	TYR- 90	2.6	139.97	H-Bond (Protein Donor)	false
O3	NH2	ARG- 121	2.99	125.12	H-Bond (Protein Donor)	false
F2	CE2	PHE- 135	3.38	0	Hydrophobic	false
F3	CZ	PHE- 137	4.36	0	Hydrophobic	false