scPDB - 1wn3 entry

Protein Data Bank Entry:

PDB ID : 1wn3

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2004-07-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phenylacetic acid degradation protein PaaI
ID:	Q5SJP3_THET8
AC:	Q5SJP3
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	39 %
C	17 %
D	44 %

Ligand binding site composition:

B-Factor:	21.697
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.095	577.125

% Hydrophobic	% Polar
48.54	51.46
According to VolSite

Ligand :

HET Code:	HXC
Formula:	C27H42N7O17P3S
Molecular weight:	861.645 g/mol
DrugBank ID:	DB02563
Buried Surface Area:	43.99 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	24

Mass center Coordinates

X	Y	Z
-12.0229	25.5243	13.5728

Binding mode :

What is Poseview ?

2D View
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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
CM6	CB	ASN- 33	3.55	0	Hydrophobic	false
CM4	CD2	LEU- 34	4.22	0	Hydrophobic	false
CM5	CB	ALA- 52	3.62	0	Hydrophobic	false
CP4	CB	VAL- 62	4.15	0	Hydrophobic	false
CM2	CG1	VAL- 62	3.91	0	Hydrophobic	false
CP8	CG2	VAL- 62	3.44	0	Hydrophobic	false
OM2	N	ALA- 63	3.18	168.97	H-Bond (Protein Donor)	false
CP8	CD2	LEU- 64	3.49	0	Hydrophobic	false
CP4	CB	TYR- 70	3.87	0	Hydrophobic	false
OP3	O	PHE- 71	2.89	157.84	H-Bond (Ligand Donor)	false
O31	NH1	ARG- 72	2.89	122.21	H-Bond (Protein Donor)	false
C1'	CG	PRO- 73	4.47	0	Hydrophobic	false
O22	OG	SER- 90	2.65	150.97	H-Bond (Protein Donor)	false
O12	N	ARG- 91	3.2	165.66	H-Bond (Protein Donor)	false
O22	N	ARG- 92	2.67	165.6	H-Bond (Protein Donor)	false
CP9	CD1	PHE- 115	4.39	0	Hydrophobic	false
CP8	CB	PHE- 115	4.07	0	Hydrophobic	false
CP9	CD2	LEU- 117	4.27	0	Hydrophobic	false