scPDB - 3akm entry

Protein Data Bank Entry:

PDB ID : 3akm

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2010-07-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Fatty acid-binding protein, intestinal
ID:	FABPI_HUMAN
AC:	P12104
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	5 %
B	95 %

Ligand binding site composition:

B-Factor:	19.948
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.202	1046.250

% Hydrophobic	% Polar
53.55	46.45
According to VolSite

Ligand :

HET Code:	11D
Formula:	C23H33N2O4S
Molecular weight:	433.584 g/mol
DrugBank ID:	-
Buried Surface Area:	77.57 %
Polar Surface area:	97.92 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
2.14647	-24.7892	27.5935

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	CE1	PHE- 17	4.42	0	Hydrophobic	false
C9	SD	MET- 18	3.52	0	Hydrophobic	false
C5	CE	MET- 21	3.98	0	Hydrophobic	false
C13	CB	VAL- 23	4.29	0	Hydrophobic	false
C3	CG1	VAL- 23	3.93	0	Hydrophobic	false
C12	CD	LYS- 27	3.88	0	Hydrophobic	false
C13	CD	LYS- 27	4.08	0	Hydrophobic	false
C9	CB	ALA- 31	3.56	0	Hydrophobic	false
C12	CE2	PHE- 55	3.32	0	Hydrophobic	false
C27	CG1	VAL- 60	4.38	0	Hydrophobic	false
C26	CD2	TYR- 70	3.86	0	Hydrophobic	false
C27	CE1	TYR- 70	3.55	0	Hydrophobic	false
C25	CE2	TYR- 70	3.97	0	Hydrophobic	false
C5	CD1	LEU- 72	3.92	0	Hydrophobic	false
C6	CB	LEU- 72	3.6	0	Hydrophobic	false
C20	CD2	LEU- 72	3.53	0	Hydrophobic	false
C12	CB	ALA- 73	3.4	0	Hydrophobic	false
C7	CB	ALA- 73	4.03	0	Hydrophobic	false
C13	CB	ASP- 74	3.55	0	Hydrophobic	false
C1	CB	ASP- 74	3.73	0	Hydrophobic	false
C21	CD1	LEU- 78	4.34	0	Hydrophobic	false
C24	CD1	LEU- 78	3.92	0	Hydrophobic	false
C25	CZ2	TRP- 82	4.21	0	Hydrophobic	false
O29	NE1	TRP- 82	2.79	152.53	H-Bond (Protein Donor)	false
C23	CD2	PHE- 93	4.12	0	Hydrophobic	false
C26	CZ	PHE- 93	4.23	0	Hydrophobic	false
C24	CE2	PHE- 93	3.69	0	Hydrophobic	false
C21	CD1	LEU- 102	3.9	0	Hydrophobic	false
C23	CD2	LEU- 102	4.35	0	Hydrophobic	false
C23	CG2	THR- 104	4.33	0	Hydrophobic	false
O30	NH1	ARG- 106	2.93	137.23	H-Bond (Protein Donor)	false
O30	NH2	ARG- 106	2.95	136.59	H-Bond (Protein Donor)	false
O30	CZ	ARG- 106	3.35	0	Ionic (Protein Cationic)	false
C19	CE1	TYR- 117	3.66	0	Hydrophobic	false