scPDB - 4i58 entry

Protein Data Bank Entry:

PDB ID : 4i58

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2012-11-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclohexylamine Oxidase
ID:	R4GRV2_9MICO
AC:	R4GRV2
Organism:	Microbacterium oxydans
Reign:	Bacteria
TaxID:	82380
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.104
Number of residues:	66
Including
Standard Amino Acids:	66
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.340	1036.125

% Hydrophobic	% Polar
53.75	46.25
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	74.66 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
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
81.6732	-58.6138	145.755

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
C4'	CD1	ILE- 41	3.72	0	Hydrophobic	false
O1P	N	SER- 42	3.2	150.97	H-Bond (Protein Donor)	false
O3B	OE1	GLU- 61	3.47	152.78	H-Bond (Ligand Donor)	false
O3B	OE2	GLU- 61	2.73	149.78	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 61	2.66	161.27	H-Bond (Ligand Donor)	false
C1B	CB	ALA- 62	4.37	0	Hydrophobic	false
O1A	NH1	ARG- 69	2.73	132.3	H-Bond (Protein Donor)	false
O2A	N	ARG- 69	2.65	155.23	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 69	3.83	0	Ionic (Protein Cationic)	false
C8M	CB	ARG- 69	4.49	0	Hydrophobic	false
C9	CB	ARG- 69	4.4	0	Hydrophobic	false
C4'	CB	ARG- 69	4.37	0	Hydrophobic	false
C5'	CG	ARG- 69	4.49	0	Hydrophobic	false
C2'	CB	ARG- 69	4.27	0	Hydrophobic	false
N3	O	PHE- 88	3.14	140.27	H-Bond (Ligand Donor)	false
O4	N	PHE- 88	2.92	150.02	H-Bond (Protein Donor)	false
N6A	O	VAL- 263	3.04	172.06	H-Bond (Ligand Donor)	false
N1A	N	VAL- 263	2.96	162.59	H-Bond (Protein Donor)	false
C5B	CB	MET- 291	4.02	0	Hydrophobic	false
C7M	CD2	TYR- 321	3.65	0	Hydrophobic	false
C7M	CB	LYS- 323	3.95	0	Hydrophobic	false
C7M	CE2	TRP- 412	4.28	0	Hydrophobic	false
C8M	CD2	TRP- 412	3.82	0	Hydrophobic	false
C2B	CB	TRP- 417	4.22	0	Hydrophobic	false
C9	CB	PRO- 422	3.89	0	Hydrophobic	false
O2P	N	THR- 450	2.93	146.4	H-Bond (Protein Donor)	false
C5'	CG2	THR- 450	3.64	0	Hydrophobic	false
O3'	O	GLY- 458	2.83	137.17	H-Bond (Ligand Donor)	false
N1	N	MET- 460	3.42	131.9	H-Bond (Protein Donor)	false
O2	N	MET- 460	2.74	166.14	H-Bond (Protein Donor)	false
C2'	CG	MET- 460	4.02	0	Hydrophobic	false