scPDB - 1opm entry

Protein Data Bank Entry:

PDB ID : 1opm

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 1999-05-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Peptidyl-glycine alpha-amidating monooxygenase
ID:	AMD_RAT
AC:	P14925
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	1.14.17.3

Chains:

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

Ligand binding site composition:

B-Factor:	33.162
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	CU

Cavity properties

Ligandability	Volume (Å3)
1.212	1343.250

% Hydrophobic	% Polar
41.71	58.29
According to VolSite

Ligand :

HET Code:	IYG
Formula:	C13H12I2N2O5
Molecular weight:	530.054 g/mol
DrugBank ID:	DB02598
Buried Surface Area:	52.47 %
Polar Surface area:	121.39 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
44.3515	24.5695	43.1087

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
I1	CE2	PHE- 112	3.73	0	Hydrophobic	false
I2	CG	LYS- 134	3.42	0	Hydrophobic	false
OH	O	ALA- 135	2.67	161.88	H-Bond (Ligand Donor)	false
I1	CB	ALA- 135	4.16	0	Hydrophobic	false
I1	CB	ILE- 137	4.24	0	Hydrophobic	false
CD2	CD2	LEU- 206	3.65	0	Hydrophobic	false
CAN	CE	MET- 208	3.42	0	Hydrophobic	false
CD2	SD	MET- 208	3.63	0	Hydrophobic	false
OT1	NH2	ARG- 240	2.86	176.07	H-Bond (Protein Donor)	false
OT2	NH2	ARG- 240	3.49	127.55	H-Bond (Protein Donor)	false
OT2	NH1	ARG- 240	2.76	160.01	H-Bond (Protein Donor)	false
OT1	CZ	ARG- 240	3.71	0	Ionic (Protein Cationic)	false
OT2	CZ	ARG- 240	3.55	0	Ionic (Protein Cationic)	false
CAN	CG2	ILE- 306	4.28	0	Hydrophobic	false
CAN	CE	MET- 314	3.96	0	Hydrophobic	false
ON	ND2	ASN- 316	3.15	179.51	H-Bond (Protein Donor)	false
NT	OD1	ASN- 316	2.95	154.05	H-Bond (Ligand Donor)	false
CB	CZ	TYR- 318	4.43	0	Hydrophobic	false
I1	CE2	TYR- 318	4.34	0	Hydrophobic	false
OT2	OH	TYR- 318	2.62	123.94	H-Bond (Protein Donor)	false