scPDB - 1s9d entry

Protein Data Bank Entry:

PDB ID : 1s9d

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2004-02-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cytohesin-2	ADP-ribosylation factor 1
ID:	CYH2_HUMAN	ARF1_BOVIN
AC:	Q99418	P84080
Organism:	Homo sapiens	Bos taurus
Reign:	Eukaryota
TaxID:	9606	9913
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	53 %
E	47 %

Ligand binding site composition:

B-Factor:	16.206
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.655	685.125

% Hydrophobic	% Polar
50.25	49.75
According to VolSite

Ligand :

HET Code:	AFB
Formula:	C16H24O4
Molecular weight:	280.359 g/mol
DrugBank ID:	DB07348
Buried Surface Area:	78.33 %
Polar Surface area:	66.76 Å2

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

Mass center Coordinates

X	Y	Z
26.6495	10.581	31.064

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
C16	SD	MET- 18	3.7	0	Hydrophobic	false
C8	CZ	PHE- 51	4.11	0	Hydrophobic	false
C6	CD1	PHE- 51	3.92	0	Hydrophobic	false
C4	CD2	TRP- 66	3.66	0	Hydrophobic	false
C9	CZ2	TRP- 66	3.88	0	Hydrophobic	false
C6	CB	ASP- 67	4.22	0	Hydrophobic	false
OC4	N	ASP- 67	2.86	169.57	H-Bond (Protein Donor)	false
OC7	NE1	TRP- 78	3.11	133.16	H-Bond (Protein Donor)	false
C7	CE2	TRP- 78	3.94	0	Hydrophobic	false
C12	CZ	TYR- 81	4.27	0	Hydrophobic	false
C16	CD1	TYR- 81	3.9	0	Hydrophobic	false
C14	CE1	TYR- 81	3.51	0	Hydrophobic	false
C6	CB	ALA- 157	4.13	0	Hydrophobic	false
OC7	OH	TYR- 190	2.7	132.38	H-Bond (Ligand Donor)	false
C8	CE2	TYR- 190	4.07	0	Hydrophobic	false
C8	CG	MET- 194	3.81	0	Hydrophobic	false
C9	CE	MET- 194	4.35	0	Hydrophobic	false
C12	CB	MET- 194	3.86	0	Hydrophobic	false
C12	CB	THR- 197	4.31	0	Hydrophobic	false
C13	CG2	THR- 197	3.91	0	Hydrophobic	false
C13	CB	ASP- 198	4.12	0	Hydrophobic	false
C13	CG2	VAL- 204	4.17	0	Hydrophobic	false
C14	CG1	VAL- 204	4.16	0	Hydrophobic	false
C15	CG2	VAL- 204	3.96	0	Hydrophobic	false
C16	CG1	VAL- 204	3.97	0	Hydrophobic	false
OC7	O	HOH- 438	2.7	161.22	H-Bond (Protein Donor)	false