scPDB - 4ymk entry

Protein Data Bank Entry:

PDB ID : 4ymk

Resolution :2.610 Å

Experimental Method : X-ray

Deposition Date : 2015-03-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acyl-CoA desaturase 1
ID:	ACOD1_MOUSE
AC:	P13516
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	35.588
Number of residues:	63
Including
Standard Amino Acids:	58
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	ZN ZN

Cavity properties

Ligandability	Volume (Å3)
1.422	951.750

% Hydrophobic	% Polar
62.41	37.59
According to VolSite

Ligand :

HET Code:	ST9
Formula:	C39H66N7O17P3S
Molecular weight:	1029.964 g/mol
DrugBank ID:	-
Buried Surface Area:	57.74 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	36

Mass center Coordinates

X	Y	Z
-30.7364	-26.9548	10.917

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
CEP	CG2	VAL- 68	3.74	0	Hydrophobic	false
O9P	ND2	ASN- 71	2.7	153.35	H-Bond (Protein Donor)	false
C18	CZ	TYR- 104	4.35	0	Hydrophobic	false
C18	CB	ALA- 108	3.73	0	Hydrophobic	false
C15	CG2	ILE- 111	3.64	0	Hydrophobic	false
C15	CG2	THR- 112	3.63	0	Hydrophobic	false
C15	CG2	THR- 112	3.63	0	Hydrophobic	false
C2	CB	GLN- 143	3.54	0	Hydrophobic	false
S1P	CB	GLN- 143	4.23	0	Hydrophobic	false
N4P	OD1	ASN- 144	3.1	164.09	H-Bond (Ligand Donor)	false
C5	CE2	TRP- 149	3.65	0	Hydrophobic	false
C11	CH2	TRP- 149	3.81	0	Hydrophobic	false
C7	CZ2	TRP- 149	3.63	0	Hydrophobic	false
O7A	NH1	ARG- 151	3.15	129.47	H-Bond (Protein Donor)	false
O7A	NH2	ARG- 151	2.7	148.4	H-Bond (Protein Donor)	false
O7A	CZ	ARG- 151	3.33	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 151	3.89	162.19	Pi/Cation	false
N6A	OD1	ASP- 152	2.56	134.08	H-Bond (Ligand Donor)	false
C3	CZ2	TRP- 180	3.45	0	Hydrophobic	false
S1P	CD2	LEU- 181	4.16	0	Hydrophobic	false
C2P	CD1	LEU- 181	4.39	0	Hydrophobic	false
O4A	CZ	ARG- 184	3.67	0	Ionic (Protein Cationic)	false
O6A	NH1	ARG- 184	3.43	155.76	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 185	3.63	0	Ionic (Protein Cationic)	false
O5A	N	LYS- 185	2.86	153.98	H-Bond (Protein Donor)	false
N7A	NZ	LYS- 185	3.08	145.14	H-Bond (Protein Donor)	false
CCP	CG	LYS- 185	3.71	0	Hydrophobic	false
C1B	CG	LYS- 190	3.94	0	Hydrophobic	false
C18	CG1	VAL- 253	4.38	0	Hydrophobic	false
C2P	CD2	LEU- 254	4.28	0	Hydrophobic	false
C18	CB	ALA- 256	4.18	0	Hydrophobic	false
C14	CG2	THR- 257	3.81	0	Hydrophobic	false
C16	CB	THR- 257	4.01	0	Hydrophobic	false
C7	CG2	THR- 257	3.83	0	Hydrophobic	false
O2	NE1	TRP- 258	3.08	162.67	H-Bond (Protein Donor)	false
C14	CG2	VAL- 260	3.83	0	Hydrophobic	false
C12	CG1	VAL- 260	3.66	0	Hydrophobic	false
C16	CB	ALA- 288	3.66	0	Hydrophobic	false
C12	CB	GLU- 291	4.08	0	Hydrophobic	false
C14	CG	GLU- 291	3.82	0	Hydrophobic	false