scPDB - 1akc entry

Protein Data Bank Entry:

PDB ID : 1akc

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 1994-02-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aspartate aminotransferase, mitochondrial
ID:	AATM_CHICK
AC:	P00508
Organism:	Gallus gallus
Reign:	Eukaryota
TaxID:	9031
EC Number:	2.6.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	31.171
Number of residues:	39
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.204	644.625

% Hydrophobic	% Polar
46.07	53.93
According to VolSite

Ligand :

HET Code:	PPE
Formula:	C13H16N2O9P
Molecular weight:	375.248 g/mol
DrugBank ID:	DB01813
Buried Surface Area:	75.78 %
Polar Surface area:	212.22 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
45.8156	13.4913	42.1168

Binding mode :

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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
CGA	CG2	ILE- 17	4.3	0	Hydrophobic	false
CGA	CD1	LEU- 18	4.07	0	Hydrophobic	false
CGA	CG2	VAL- 37	3.73	0	Hydrophobic	false
OXT	N	GLY- 38	2.78	149.54	H-Bond (Protein Donor)	false
OP1	N	GLY- 108	2.86	155.32	H-Bond (Protein Donor)	false
OP3	OG1	THR- 109	2.59	153.13	H-Bond (Protein Donor)	false
OP3	N	THR- 109	2.84	163.71	H-Bond (Protein Donor)	false
C2A	CE3	TRP- 140	4.13	0	Hydrophobic	false
C5A	CH2	TRP- 140	3.51	0	Hydrophobic	false
OE1	NE1	TRP- 140	2.9	148.92	H-Bond (Protein Donor)	false
DuAr	DuAr	TRP- 140	3.52	0	Aromatic Face/Face	false
C2A	CB	ASN- 194	3.91	0	Hydrophobic	false
O3	ND2	ASN- 194	2.52	142.57	H-Bond (Protein Donor)	false
OA	ND2	ASN- 194	2.73	150.93	H-Bond (Protein Donor)	false
N1	OD2	ASP- 222	2.67	165.81	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 222	3.33	134.49	H-Bond (Ligand Donor)	false
C2A	CB	ALA- 224	4.25	0	Hydrophobic	false
C5	CB	ALA- 224	3.98	0	Hydrophobic	false
C2A	CE2	TYR- 225	4.13	0	Hydrophobic	false
OP1	OG	SER- 255	3.09	152.87	H-Bond (Protein Donor)	false
OP2	NH2	ARG- 266	3.38	138.39	H-Bond (Protein Donor)	false
OP2	NH1	ARG- 266	2.92	164.87	H-Bond (Protein Donor)	false
OP3	NH2	ARG- 266	2.93	146.51	H-Bond (Protein Donor)	false
OP2	CZ	ARG- 266	3.64	0	Ionic (Protein Cationic)	false
OP3	CZ	ARG- 266	3.86	0	Ionic (Protein Cationic)	false
OA	NH2	ARG- 386	3.17	132.71	H-Bond (Protein Donor)	false
OA	NH1	ARG- 386	2.71	158.4	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 386	2.61	139.23	H-Bond (Protein Donor)	false
OA	CZ	ARG- 386	3.36	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 386	3.57	0	Ionic (Protein Cationic)	false