scPDB - 1akb entry

Protein Data Bank Entry:

PDB ID : 1akb

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:	24.157
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.349	425.250

% Hydrophobic	% Polar
49.21	50.79
According to VolSite

Ligand :

HET Code:	PPD
Formula:	C12H14N2O9P
Molecular weight:	361.221 g/mol
DrugBank ID:	-
Buried Surface Area:	74.34 %
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:	9

Mass center Coordinates

X	Y	Z
45.8775	13.7347	42.6053

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
CB	CG2	VAL- 37	3.89	0	Hydrophobic	false
O	N	GLY- 38	3.09	147.94	H-Bond (Protein Donor)	false
O2P	OG	SER- 107	2.6	148.1	H-Bond (Protein Donor)	false
O2P	N	GLY- 108	2.88	154.22	H-Bond (Protein Donor)	false
O1P	N	THR- 109	2.99	161.09	H-Bond (Protein Donor)	false
O1P	OG1	THR- 109	2.68	158.16	H-Bond (Protein Donor)	false
C2A	CB	TRP- 140	4.22	0	Hydrophobic	false
C5A	CH2	TRP- 140	3.53	0	Hydrophobic	false
OD1	NE1	TRP- 140	2.98	139.68	H-Bond (Protein Donor)	false
DuAr	DuAr	TRP- 140	3.63	0	Aromatic Face/Face	false
C2A	CB	ASN- 194	3.98	0	Hydrophobic	false
O3	ND2	ASN- 194	2.62	146.92	H-Bond (Protein Donor)	false
OXT	ND2	ASN- 194	2.91	146.3	H-Bond (Protein Donor)	false
N1	OD1	ASP- 222	3.31	136.73	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 222	2.89	163.68	H-Bond (Ligand Donor)	false
C2A	CB	ALA- 224	4.23	0	Hydrophobic	false
C5	CB	ALA- 224	4.02	0	Hydrophobic	false
C2A	CE2	TYR- 225	4.11	0	Hydrophobic	false
O3	OH	TYR- 225	2.55	142.36	H-Bond (Protein Donor)	false
O2P	OG	SER- 255	2.92	161.68	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 266	2.94	157.26	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 266	3	167.84	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 266	3.78	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 266	3.78	0	Ionic (Protein Cationic)	false
O	NH2	ARG- 386	2.96	147.43	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 386	3.32	134.17	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 386	2.84	156.82	H-Bond (Protein Donor)	false
O	CZ	ARG- 386	3.9	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 386	3.54	0	Ionic (Protein Cationic)	false