scPDB - 3wd2 entry

Protein Data Bank Entry:

PDB ID : 3wd2

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2013-06-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Chitinase B
ID:	CHIB_SERMA
AC:	P11797
Organism:	Serratia marcescens
Reign:	Bacteria
TaxID:	615
EC Number:	3.2.1.14

Chains:

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

Ligand binding site composition:

B-Factor:	26.595
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.161	810.000

% Hydrophobic	% Polar
44.17	55.83
According to VolSite

Ligand :

HET Code:	A1L
Formula:	C24H32N9O3
Molecular weight:	494.569 g/mol
DrugBank ID:	-
Buried Surface Area:	56.8 %
Polar Surface area:	177.9 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	5
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
-21.7045	1.70069	-29.0829

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
C6	CE3	TRP- 97	4.32	0	Hydrophobic	false
C5	CB	TRP- 97	4.47	0	Hydrophobic	false
C4	CD2	TRP- 97	4.01	0	Hydrophobic	false
N4	OE2	GLU- 144	2.74	164.84	H-Bond (Ligand Donor)	false
N3	OE2	GLU- 144	3.35	135.47	H-Bond (Ligand Donor)	false
N3	OE1	GLU- 144	2.71	159.21	H-Bond (Ligand Donor)	false
O3	OH	TYR- 214	2.82	164.67	H-Bond (Protein Donor)	false
C21	CG	PRO- 219	3.52	0	Hydrophobic	false
O2	NH2	ARG- 294	2.7	149.86	H-Bond (Protein Donor)	false
C18	CB	ASP- 316	4.49	0	Hydrophobic	false
C21	CD	ARG- 338	3.79	0	Hydrophobic	false
C22	CB	ARG- 338	3.94	0	Hydrophobic	false
C23	CG1	ILE- 339	4.21	0	Hydrophobic	false
N9	NE1	TRP- 403	3.01	130.25	H-Bond (Protein Donor)	false