scPDB - 3koy entry

Protein Data Bank Entry:

PDB ID : 3koy

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2009-11-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	D-ornithine 4,5-aminomutase subunit beta
ID:	OAME_CLOSD
AC:	E3PY95
Organism:	Clostridium sticklandii
Reign:	Bacteria
TaxID:	499177
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	92 %
C	8 %

Ligand binding site composition:

B-Factor:	26.183
Number of residues:	38
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.712	901.125

% Hydrophobic	% Polar
33.33	66.67
According to VolSite

Ligand :

HET Code:	Z97
Formula:	C13H18N3O7P
Molecular weight:	359.272 g/mol
DrugBank ID:	-
Buried Surface Area:	70.99 %
Polar Surface area:	195.48 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-6.81667	99.5074	23.5592

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
N	OE2	GLU- 81	3.3	148.79	H-Bond (Ligand Donor)	false
N	OE2	GLU- 81	3.3	0	Ionic (Ligand Cationic)	false
CB	CD1	ILE- 108	3.85	0	Hydrophobic	false
OP3	CZ	ARG- 109	3.23	0	Ionic (Protein Cationic)	false
OP3	NH2	ARG- 109	2.58	132.58	H-Bond (Protein Donor)	false
OP1	N	GLY- 112	3.42	144.17	H-Bond (Protein Donor)	false
OP2	OG	SER- 114	2.61	165.38	H-Bond (Protein Donor)	false
OP3	N	SER- 114	2.94	125.71	H-Bond (Protein Donor)	false
OXT	OH	TYR- 160	2.77	165.99	H-Bond (Protein Donor)	false
N1	OG	SER- 162	2.84	156.44	H-Bond (Protein Donor)	false
C2A	CB	HIS- 182	3.88	0	Hydrophobic	false
OXT	NE2	HIS- 182	3	130.1	H-Bond (Protein Donor)	false
C2A	CG	TYR- 187	3.69	0	Hydrophobic	false
C5A	CZ	TYR- 187	4.05	0	Hydrophobic	false
OP2	OH	TYR- 187	2.78	167.29	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 187	3.56	0	Aromatic Face/Face	false
OP1	CZ	ARG- 192	3.82	0	Ionic (Protein Cationic)	false
OP2	CZ	ARG- 192	3.77	0	Ionic (Protein Cationic)	false
OP1	NH2	ARG- 192	2.9	141	H-Bond (Protein Donor)	false
OP2	NE	ARG- 192	3.06	147.1	H-Bond (Protein Donor)	false
O3	NE2	HIS- 225	2.9	130.79	H-Bond (Protein Donor)	false
O3	ND2	ASN- 226	2.76	158.96	H-Bond (Protein Donor)	false
NE	OD1	ASN- 226	3.38	147.97	H-Bond (Ligand Donor)	false
O	NH1	ARG- 297	2.71	151.93	H-Bond (Protein Donor)	false
O	NH2	ARG- 297	2.99	136.52	H-Bond (Protein Donor)	false
O	CZ	ARG- 297	3.28	0	Ionic (Protein Cationic)	false
O	NE2	GLN- 299	2.99	149.94	H-Bond (Protein Donor)	false