scPDB - 2d81 entry

Protein Data Bank Entry:

PDB ID : 2d81

Resolution :1.660 Å

Experimental Method : X-ray

Deposition Date : 2005-11-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Poly(3-hydroxybutyrate) depolymerase
ID:	B2NHN2_TALFU
AC:	B2NHN2
Organism:	Talaromyces funiculosus
Reign:	Eukaryota
TaxID:	28572
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	8.909
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.898	391.500

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	RB3
Formula:	C13H22O7
Molecular weight:	290.310 g/mol
DrugBank ID:	DB04773
Buried Surface Area:	61.33 %
Polar Surface area:	99.13 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
17.8044	-8.42474	28.2926

Binding mode :

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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
C4A	CB	ALA- 39	4.09	0	Hydrophobic	false
C4A	CB	SER- 40	4.36	0	Hydrophobic	false
C4A	CD2	TYR- 43	4.32	0	Hydrophobic	false
C4B	CD1	TYR- 76	3.73	0	Hydrophobic	false
C3B	CE1	TYR- 76	4.26	0	Hydrophobic	false
C2B	SD	MET- 80	4.18	0	Hydrophobic	false
C2A	CE	MET- 80	4.08	0	Hydrophobic	false
C2A	CG2	THR- 123	3.98	0	Hydrophobic	false
C2A	CG2	VAL- 124	4.24	0	Hydrophobic	false
C4A	CG2	VAL- 124	4	0	Hydrophobic	false
C3A	SG	CYS- 250	3.86	0	Hydrophobic	false
C2B	SG	CYS- 250	4.4	0	Hydrophobic	false
C4B	CD2	LEU- 298	4.44	0	Hydrophobic	false
C2C	CD2	LEU- 298	3.97	0	Hydrophobic	false
C4C	CD1	LEU- 298	4.35	0	Hydrophobic	false
C4C	CG	PRO- 301	3.59	0	Hydrophobic	false
C3B	SG	CYS- 304	4.09	0	Hydrophobic	false
C4A	CZ2	TRP- 307	3.84	0	Hydrophobic	false
C4B	CZ2	TRP- 307	3.65	0	Hydrophobic	false
O1B	NE1	TRP- 307	2.94	157.23	H-Bond (Protein Donor)	false
C4B	CG1	VAL- 308	3.8	0	Hydrophobic	false
C2C	CZ2	TRP- 310	3.93	0	Hydrophobic	false
C4B	CH2	TRP- 310	3.8	0	Hydrophobic	false
O1C	O	HOH- 516	3.13	179.97	H-Bond (Protein Donor)	false
O1A	O	HOH- 528	2.79	179.95	H-Bond (Protein Donor)	false