scPDB - 2iid entry

Protein Data Bank Entry:

PDB ID : 2iid

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2006-09-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	L-amino-acid oxidase
ID:	OXLA_CALRH
AC:	P81382
Organism:	Calloselasma rhodostoma
Reign:	Eukaryota
TaxID:	8717
EC Number:	1.4.3.2

Chains:

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

Ligand binding site composition:

B-Factor:	11.464
Number of residues:	75
Including
Standard Amino Acids:	69
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.596	469.125

% Hydrophobic	% Polar
54.68	45.32
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	80.38 %
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
19.9803	103.926	71.1855

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
O2P	N	ALA- 44	3.02	165.24	H-Bond (Protein Donor)	false
O3B	OE1	GLU- 63	2.76	164.17	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 63	2.62	157.13	H-Bond (Ligand Donor)	false
N3A	N	ALA- 64	3.05	130.23	H-Bond (Protein Donor)	false
O1A	NE	ARG- 71	2.8	165.56	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 71	3.44	129.58	H-Bond (Protein Donor)	false
O2A	N	ARG- 71	2.69	172.77	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 71	3.28	153.14	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 71	3.54	0	Ionic (Protein Cationic)	false
C8M	CD	ARG- 71	3.99	0	Hydrophobic	false
C9A	CG	PRO- 88	4.05	0	Hydrophobic	false
C2'	CG	PRO- 88	3.92	0	Hydrophobic	false
O4	N	MET- 89	2.89	172.77	H-Bond (Protein Donor)	false
N3	O	ARG- 90	2.84	161.69	H-Bond (Ligand Donor)	false
O4	N	ARG- 90	3.09	151.16	H-Bond (Protein Donor)	false
N6A	O	VAL- 261	3.08	158.99	H-Bond (Ligand Donor)	false
N1A	N	VAL- 261	2.93	163	H-Bond (Protein Donor)	false
C1B	CG2	THR- 294	4.42	0	Hydrophobic	false
C7M	CE1	TYR- 372	4.17	0	Hydrophobic	false
C8M	CD2	TRP- 420	4.06	0	Hydrophobic	false
C2B	CB	TYR- 425	3.82	0	Hydrophobic	false
C9A	CD1	ILE- 430	4.17	0	Hydrophobic	false
C7	CD1	ILE- 430	3.76	0	Hydrophobic	false
C8	CG1	ILE- 430	3.58	0	Hydrophobic	false
O3'	OE2	GLU- 457	2.72	158.15	H-Bond (Ligand Donor)	false
C5'	CB	GLU- 457	4.16	0	Hydrophobic	false
O1P	N	GLU- 457	2.81	158.44	H-Bond (Protein Donor)	false
N1	N	ILE- 466	3.3	137.13	H-Bond (Protein Donor)	false
O2	N	ILE- 466	2.72	160.69	H-Bond (Protein Donor)	false
C2'	CG1	ILE- 466	4.14	0	Hydrophobic	false
O3'	OG1	THR- 469	2.91	155.18	H-Bond (Protein Donor)	false
C5'	CG2	THR- 469	3.8	0	Hydrophobic	false
C6	CB	PHE- 524	4.41	0	Hydrophobic	false
C9A	CB	PHE- 524	4.5	0	Hydrophobic	false
O2P	O	HOH- 526	2.66	179.97	H-Bond (Protein Donor)	false
O2A	O	HOH- 527	2.57	154.29	H-Bond (Protein Donor)	false
O2	O	HOH- 535	2.85	179.99	H-Bond (Protein Donor)	false
O3B	O	HOH- 557	2.92	179.98	H-Bond (Protein Donor)	false