scPDB - 4ynt entry

Protein Data Bank Entry:

PDB ID : 4ynt

Resolution :1.780 Å

Experimental Method : X-ray

Deposition Date : 2015-03-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glucose oxidase, putative
ID:	B8MX95_ASPFN
AC:	B8MX95
Organism:	Aspergillus flavus
Reign:	Eukaryota
TaxID:	332952
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.947
Number of residues:	65
Including
Standard Amino Acids:	61
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.255	837.000

% Hydrophobic	% Polar
53.63	46.37
According to VolSite

Ligand :

HET Code:	FDA
Formula:	C27H33N9O15P2
Molecular weight:	785.550 g/mol
DrugBank ID:	-
Buried Surface Area:	80.02 %
Polar Surface area:	381.04 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	9
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
27.7487	39.5325	54.1324

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
O2A	OG1	THR- 15	2.66	162.26	H-Bond (Protein Donor)	false
O2A	N	THR- 15	3.17	168.2	H-Bond (Protein Donor)	false
O4'	OG1	THR- 15	2.77	165.13	H-Bond (Ligand Donor)	false
C4'	CB	THR- 15	4.25	0	Hydrophobic	false
O1P	N	SER- 16	3.03	147.97	H-Bond (Protein Donor)	false
O1P	OG	SER- 16	2.8	159.83	H-Bond (Protein Donor)	false
O3B	OE1	GLU- 36	2.68	165.02	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 36	2.73	140.48	H-Bond (Ligand Donor)	false
N3A	N	ALA- 37	3.25	138.13	H-Bond (Protein Donor)	false
C7M	CE1	TYR- 53	4.09	0	Hydrophobic	false
C7M	CZ	PHE- 57	3.48	0	Hydrophobic	false
C2B	CE2	TRP- 63	4.33	0	Hydrophobic	false
O2B	NE1	TRP- 63	3.17	145.4	H-Bond (Protein Donor)	false
C8M	CB	ARG- 81	4.06	0	Hydrophobic	false
O1A	OG1	THR- 89	2.64	169.07	H-Bond (Protein Donor)	false
O2A	N	THR- 89	2.9	167.73	H-Bond (Protein Donor)	false
C8M	CG2	THR- 89	3.52	0	Hydrophobic	false
C9	CG2	THR- 89	3.55	0	Hydrophobic	false
C3'	CG2	THR- 89	3.93	0	Hydrophobic	false
C4'	CB	THR- 89	4.12	0	Hydrophobic	false
C8M	CD1	ILE- 92	4.44	0	Hydrophobic	false
O2'	ND2	ASN- 93	3.08	149.31	H-Bond (Protein Donor)	false
C9A	CB	ASN- 93	3.48	0	Hydrophobic	false
N5	N	GLY- 94	3.15	163.28	H-Bond (Protein Donor)	false
N3	O	ALA- 96	2.89	157.84	H-Bond (Ligand Donor)	false
O4	N	ALA- 96	2.96	160.41	H-Bond (Protein Donor)	false
N6A	O	ALA- 235	2.88	162.66	H-Bond (Ligand Donor)	false
N1A	N	ALA- 235	2.96	151.9	H-Bond (Protein Donor)	false
C7M	CD2	PHE- 504	3.42	0	Hydrophobic	false
C8	CB	PHE- 504	3.41	0	Hydrophobic	false
O2P	N	ALA- 538	3.16	172.18	H-Bond (Protein Donor)	false
C3'	CB	LEU- 549	4.28	0	Hydrophobic	false
O2	N	VAL- 550	2.94	155.83	H-Bond (Protein Donor)	false
C2'	CG1	VAL- 550	3.63	0	Hydrophobic	false
C5'	CD1	LEU- 553	3.47	0	Hydrophobic	false
O1P	O	HOH- 786	3.01	167.21	H-Bond (Protein Donor)	false
N5	O	HOH- 798	2.92	179.95	H-Bond (Protein Donor)	false
O2	O	HOH- 916	2.91	179.96	H-Bond (Protein Donor)	false