scPDB - 4l1f entry

Protein Data Bank Entry:

PDB ID : 4l1f

Resolution :1.790 Å

Experimental Method : X-ray

Deposition Date : 2013-06-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acyl-CoA dehydrogenase domain protein
ID:	D2RL84_ACIFV
AC:	D2RL84
Organism:	Acidaminococcus fermentans
Reign:	Bacteria
TaxID:	591001
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	3 %
B	97 %

Ligand binding site composition:

B-Factor:	17.218
Number of residues:	42
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.159	577.125

% Hydrophobic	% Polar
42.11	57.89
According to VolSite

Ligand :

HET Code:	COS
Formula:	C21H32N7O16P3S2
Molecular weight:	795.567 g/mol
DrugBank ID:	DB04036
Buried Surface Area:	49.01 %
Polar Surface area:	451.41 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
126.574	2.50929	-25.4858

Binding mode :

What is Poseview ?

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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
C2P	CE2	PHE- 123	4.38	0	Hydrophobic	false
S1P	CD2	PHE- 123	4.07	0	Hydrophobic	false
C2P	CD2	LEU- 125	4.46	0	Hydrophobic	false
CDP	CG2	THR- 132	4.49	0	Hydrophobic	false
N8P	O	THR- 132	3	156.97	H-Bond (Ligand Donor)	false
C6P	CB	ALA- 134	3.98	0	Hydrophobic	false
C5B	CG2	VAL- 178	4.03	0	Hydrophobic	false
O7A	NE2	HIS- 179	3.21	154.3	H-Bond (Protein Donor)	false
O9A	NE2	HIS- 179	3.22	134.55	H-Bond (Protein Donor)	false
C1B	CD2	PHE- 232	4.24	0	Hydrophobic	false
C4B	CD2	PHE- 232	3.82	0	Hydrophobic	false
C5B	CE2	PHE- 232	3.73	0	Hydrophobic	false
CAP	CZ	PHE- 232	4.48	0	Hydrophobic	false
CAP	SD	MET- 236	3.87	0	Hydrophobic	false
C6P	CD1	LEU- 239	4.32	0	Hydrophobic	false
S1P	CD2	LEU- 239	3.64	0	Hydrophobic	false
N6A	OD2	ASP- 240	2.84	154.68	H-Bond (Ligand Donor)	false
O9P	NH2	ARG- 243	2.96	149.18	H-Bond (Protein Donor)	false
O5P	NH2	ARG- 243	2.98	157.84	H-Bond (Protein Donor)	false
CDP	CZ	PHE- 271	4.21	0	Hydrophobic	false
S'P	CB	TYR- 362	3.86	0	Hydrophobic	false
S1P	CG	GLU- 363	4.14	0	Hydrophobic	false
S'P	CG	GLU- 363	3.46	0	Hydrophobic	false
CDP	CG1	VAL- 368	4.35	0	Hydrophobic	false
CEP	CG1	VAL- 368	3.98	0	Hydrophobic	false
CEP	CG2	VAL- 372	4.18	0	Hydrophobic	false
O1A	CZ	ARG- 375	3.62	0	Ionic (Protein Cationic)	false
O5A	CZ	ARG- 375	3.81	0	Ionic (Protein Cationic)	false
O1A	NH1	ARG- 375	2.73	132.8	H-Bond (Protein Donor)	false
O5A	NH2	ARG- 375	2.88	171.56	H-Bond (Protein Donor)	false
S'P	C9A	FAD- 401	4	0	Hydrophobic	false
O4A	O	HOH- 529	2.81	156.57	H-Bond (Protein Donor)	false
O9P	O	HOH- 538	2.88	179.97	H-Bond (Protein Donor)	false
N4P	O	HOH- 553	2.93	172.49	H-Bond (Ligand Donor)	false