scPDB - 3in9 entry

Protein Data Bank Entry:

PDB ID : 3in9

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2009-08-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Heparin lyase I
ID:	Q89YQ6_BACTN
AC:	Q89YQ6
Organism:	Bacteroides thetaiotaomicron
Reign:	Bacteria
TaxID:	226186
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.497
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.527	1198.125

% Hydrophobic	% Polar
33.52	66.48
According to VolSite

Ligand :

HET Code:	H1S
Formula:	C12H15NO19S3
Molecular weight:	573.438 g/mol
DrugBank ID:	DB02322
Buried Surface Area:	47.15 %
Polar Surface area:	355.74 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	4
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
37.6397	1.948	13.5523

Binding mode :

What is Poseview ?

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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
O21	ND2	ASN- 20	3.09	148.33	H-Bond (Protein Donor)	false
O22	ND2	ASN- 20	2.76	131.79	H-Bond (Protein Donor)	false
C17	CD2	LEU- 72	4.28	0	Hydrophobic	false
O34	NZ	LYS- 81	2.76	173.38	H-Bond (Protein Donor)	false
O35	NZ	LYS- 81	3.39	120.47	H-Bond (Protein Donor)	false
O34	NZ	LYS- 81	2.76	0	Ionic (Protein Cationic)	false
O35	NZ	LYS- 81	3.39	0	Ionic (Protein Cationic)	false
O13	NH1	ARG- 83	3.33	131.2	H-Bond (Protein Donor)	false
O31	NE	ARG- 83	3.41	132.63	H-Bond (Protein Donor)	false
O23	NZ	LYS- 111	3.51	0	Ionic (Protein Cationic)	false
O28	CZ	ARG- 156	3.2	0	Ionic (Protein Cationic)	false
O29	CZ	ARG- 156	3.69	0	Ionic (Protein Cationic)	false
O28	NH1	ARG- 156	2.73	121.29	H-Bond (Protein Donor)	false
O29	NH2	ARG- 156	2.64	133.2	H-Bond (Protein Donor)	false
O35	NZ	LYS- 185	3.92	0	Ionic (Protein Cationic)	false
C10	CG	GLN- 223	4.28	0	Hydrophobic	false
O15	NE2	GLN- 223	2.84	143.86	H-Bond (Protein Donor)	false
O28	N	GLY- 224	2.97	170.45	H-Bond (Protein Donor)	false
O29	O	HOH- 417	2.71	179.99	H-Bond (Protein Donor)	false