scPDB - 4geb entry

Protein Data Bank Entry:

PDB ID : 4geb

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2012-08-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial
ID:	AADAT_HUMAN
AC:	Q8N5Z0
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.6.1.39

Chains:

Chain Name:	Percentage of Residues within binding site
A	68 %
B	32 %

Ligand binding site composition:

B-Factor:	26.309
Number of residues:	51
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.552	789.750

% Hydrophobic	% Polar
55.98	44.02
According to VolSite

Ligand :

HET Code:	0LD
Formula:	C20H17N5O7P
Molecular weight:	470.352 g/mol
DrugBank ID:	-
Buried Surface Area:	72.04 %
Polar Surface area:	188.57 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
5.56124	6.01145	-52.7661

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
C31	CD1	ILE- 19	3.62	0	Hydrophobic	false
C33	CD2	LEU- 40	3.42	0	Hydrophobic	false
O27	OH	TYR- 74	2.59	157.53	H-Bond (Protein Donor)	false
C29	CB	TYR- 74	3.65	0	Hydrophobic	false
O6	OG	SER- 117	2.91	160.64	H-Bond (Protein Donor)	false
O6	N	SER- 117	2.9	152.93	H-Bond (Protein Donor)	false
O24	OG	SER- 117	3.46	134.39	H-Bond (Protein Donor)	false
C13	CB	GLN- 118	4.05	0	Hydrophobic	false
O7	N	GLN- 118	2.89	159.22	H-Bond (Protein Donor)	false
C13	CZ	TYR- 142	4.34	0	Hydrophobic	false
C1	CG	TYR- 142	3.71	0	Hydrophobic	false
C14	CZ	TYR- 142	4.21	0	Hydrophobic	false
DuAr	DuAr	TYR- 142	3.75	0	Aromatic Face/Face	false
C1	CG2	VAL- 197	3.8	0	Hydrophobic	false
C1	CB	ASN- 202	3.99	0	Hydrophobic	false
O5	ND2	ASN- 202	2.89	144.87	H-Bond (Protein Donor)	false
O26	ND2	ASN- 202	2.84	166.41	H-Bond (Protein Donor)	false
N12	OD2	ASP- 230	2.83	174.93	H-Bond (Ligand Donor)	false
N12	OD1	ASP- 230	3.4	130.07	H-Bond (Ligand Donor)	false
C1	CG	PRO- 232	3.68	0	Hydrophobic	false
C17	CG	PRO- 232	3.84	0	Hydrophobic	false
C1	CE1	TYR- 233	4.23	0	Hydrophobic	false
O6	OG	SER- 260	2.62	164.66	H-Bond (Protein Donor)	false
O27	OG	SER- 262	2.62	178.81	H-Bond (Protein Donor)	false
O27	CZ	ARG- 270	3.64	0	Ionic (Protein Cationic)	false
O7	CZ	ARG- 270	3.68	0	Ionic (Protein Cationic)	false
O27	NH1	ARG- 270	2.87	164.72	H-Bond (Protein Donor)	false
O7	NH2	ARG- 270	2.73	164.08	H-Bond (Protein Donor)	false
O5	NH1	ARG- 399	3.35	146.94	H-Bond (Protein Donor)	false
O25	NH2	ARG- 399	3.19	174.05	H-Bond (Protein Donor)	false
O6	O	HOH- 856	3.02	172.26	H-Bond (Protein Donor)	false