scPDB - 3zw9 entry

Protein Data Bank Entry:

PDB ID : 3zw9

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2011-07-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Peroxisomal bifunctional enzyme
ID:	ECHP_RAT
AC:	P07896
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	1.1.1.35

Chains:

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

Ligand binding site composition:

B-Factor:	38.678
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.998	401.625

% Hydrophobic	% Polar
57.98	42.02
According to VolSite

Ligand :

HET Code:	T1G
Formula:	C26H40N7O18P3S
Molecular weight:	863.618 g/mol
DrugBank ID:	-
Buried Surface Area:	44.58 %
Polar Surface area:	449.91 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	22

Mass center Coordinates

X	Y	Z
-56.2745	6.47431	-114.881

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
C1'	CG	PRO- 20	3.91	0	Hydrophobic	false
C4'	CG	PRO- 20	4.22	0	Hydrophobic	false
C1'	CG2	VAL- 21	4.07	0	Hydrophobic	false
CAD	CG1	VAL- 21	4.05	0	Hydrophobic	false
CAD	CB	ALA- 59	4.5	0	Hydrophobic	false
N6	O	ALA- 61	3.41	169.15	H-Bond (Ligand Donor)	false
SBK	CB	ALA- 61	3.62	0	Hydrophobic	false
CAB	CB	ALA- 61	3.68	0	Hydrophobic	false
N1	N	ILE- 63	3.01	165.94	H-Bond (Protein Donor)	false
CAB	CZ	PHE- 66	3.68	0	Hydrophobic	false
SBK	CZ	PHE- 66	4	0	Hydrophobic	false
CAB	CG	PRO- 71	4.37	0	Hydrophobic	false
CAC	CG2	VAL- 96	3.92	0	Hydrophobic	false
CAD	CG1	VAL- 96	4.37	0	Hydrophobic	false
CAC	CD1	LEU- 98	3.34	0	Hydrophobic	false
CAX	CG	PRO- 122	4.07	0	Hydrophobic	false
CBS	CG	GLU- 123	3.53	0	Hydrophobic	false
CAW	CD1	LEU- 126	4.32	0	Hydrophobic	false
CAB	CD1	ILE- 128	3.67	0	Hydrophobic	false
OAL	N	GLY- 131	3.11	137.08	H-Bond (Protein Donor)	false
CAA	CB	ALA- 132	4.39	0	Hydrophobic	false
CAC	CE2	TYR- 156	3.97	0	Hydrophobic	false
CAA	CZ	PHE- 255	4.04	0	Hydrophobic	false
CAB	CE1	PHE- 255	4.42	0	Hydrophobic	false