scPDB - 3kp0 entry

Protein Data Bank Entry:

PDB ID : 3kp0

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	94 %
C	6 %

Ligand binding site composition:

B-Factor:	27.836
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.904	1009.125

% Hydrophobic	% Polar
42.81	57.19
According to VolSite

Ligand :

HET Code:	Z98
Formula:	C12H16N3O7P
Molecular weight:	345.245 g/mol
DrugBank ID:	-
Buried Surface Area:	67.18 %
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:	8

Mass center Coordinates

X	Y	Z
-7.957	98.0168	23.8999

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
OP1	CZ	ARG- 109	3.6	0	Ionic (Protein Cationic)	false
OP2	CZ	ARG- 109	3.35	0	Ionic (Protein Cationic)	false
OP1	NH2	ARG- 109	2.71	136.76	H-Bond (Protein Donor)	false
OP2	NH2	ARG- 109	3.13	133.98	H-Bond (Protein Donor)	false
OP2	NE	ARG- 109	2.73	158.27	H-Bond (Protein Donor)	false
OP3	OG	SER- 114	3.5	131.5	H-Bond (Protein Donor)	false
C5	CD1	TYR- 160	3.21	0	Hydrophobic	false
N1	OG	SER- 162	2.78	148.78	H-Bond (Protein Donor)	false
N	NE2	HIS- 182	2.95	151.94	H-Bond (Ligand Donor)	false
C2A	CB	HIS- 182	3.95	0	Hydrophobic	false
C2A	CB	ASP- 184	4.15	0	Hydrophobic	false
C2A	CB	TYR- 187	3.99	0	Hydrophobic	false
C5A	CZ	TYR- 187	3.8	0	Hydrophobic	false
OP3	OH	TYR- 187	3.21	122.76	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 187	3.62	0	Aromatic Face/Face	false
N	NE2	HIS- 225	2.97	159.57	H-Bond (Ligand Donor)	false
O3	ND2	ASN- 226	2.79	151.44	H-Bond (Protein Donor)	false
ND	OD1	ASN- 226	3.12	143.38	H-Bond (Ligand Donor)	false
OXT	NH2	ARG- 297	3.34	148.79	H-Bond (Protein Donor)	false
OXT	NE2	GLN- 299	2.75	146.94	H-Bond (Protein Donor)	false