scPDB - 4gdy entry

Protein Data Bank Entry:

PDB ID : 4gdy

Resolution :2.890 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	37 %
B	63 %

Ligand binding site composition:

B-Factor:	41.039
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.486	776.250

% Hydrophobic	% Polar
55.65	44.35
According to VolSite

Ligand :

HET Code:	0X1
Formula:	C24H20N5O7P
Molecular weight:	521.419 g/mol
DrugBank ID:	-
Buried Surface Area:	76.2 %
Polar Surface area:	181.3 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
8.68295	36.9869	19.1349

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
C3	CG2	ILE- 19	4.32	0	Hydrophobic	false
C31	CD	ARG- 20	3.49	0	Hydrophobic	false
O36	N	GLY- 39	2.86	164.38	H-Bond (Protein Donor)	false
C9	CD2	LEU- 40	3.64	0	Hydrophobic	false
O22	OH	TYR- 74	2.78	161.34	H-Bond (Protein Donor)	false
C2	CB	TYR- 74	4.23	0	Hydrophobic	false
C30	CB	TYR- 74	4.25	0	Hydrophobic	false
O21	OG	SER- 117	2.79	154.15	H-Bond (Protein Donor)	false
O21	N	SER- 117	2.82	156.91	H-Bond (Protein Donor)	false
O26	OG	SER- 117	3.3	136.29	H-Bond (Protein Donor)	false
C17	CB	GLN- 118	3.92	0	Hydrophobic	false
O23	N	GLN- 118	2.92	154.31	H-Bond (Protein Donor)	false
C13	CZ	TYR- 142	3.76	0	Hydrophobic	false
C16	CG	TYR- 142	3.84	0	Hydrophobic	false
DuAr	DuAr	TYR- 142	3.94	0	Aromatic Face/Face	false
C16	CG2	VAL- 197	4	0	Hydrophobic	false
C16	CB	ASN- 202	4.38	0	Hydrophobic	false
O24	ND2	ASN- 202	3.2	153.28	H-Bond (Protein Donor)	false
N37	ND2	ASN- 202	3.03	134.95	H-Bond (Protein Donor)	false
N18	OD1	ASP- 230	3.29	142.23	H-Bond (Ligand Donor)	false
N18	OD2	ASP- 230	2.78	154.39	H-Bond (Ligand Donor)	false
C10	CG	PRO- 232	4.23	0	Hydrophobic	false
C16	CG	PRO- 232	3.68	0	Hydrophobic	false
C16	CE1	TYR- 233	4.38	0	Hydrophobic	false
O22	OG	SER- 262	2.78	169.58	H-Bond (Protein Donor)	false
O22	CZ	ARG- 270	3.68	0	Ionic (Protein Cationic)	false
O23	CZ	ARG- 270	3.8	0	Ionic (Protein Cationic)	false
O22	NH1	ARG- 270	2.95	156.28	H-Bond (Protein Donor)	false
O23	NH2	ARG- 270	2.84	167.1	H-Bond (Protein Donor)	false
C32	CG	GLN- 289	4.27	0	Hydrophobic	false
C1	CD1	LEU- 293	4.03	0	Hydrophobic	false
C33	CD2	LEU- 293	4.45	0	Hydrophobic	false
C34	CD1	LEU- 293	4.44	0	Hydrophobic	false
C32	CB	LEU- 293	4.22	0	Hydrophobic	false
O36	NH2	ARG- 399	3.02	149.91	H-Bond (Protein Donor)	false