scPDB - 2cb3 entry

Protein Data Bank Entry:

PDB ID : 2cb3

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2005-12-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Peptidoglycan-recognition protein LE
ID:	PGPLE_DROME
AC:	Q9VXN9
Organism:	Drosophila melanogaster
Reign:	Eukaryota
TaxID:	7227
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	75 %
B	15 %
D	9 %

Ligand binding site composition:

B-Factor:	23.236
Number of residues:	55
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.743	1680.750

% Hydrophobic	% Polar
35.14	64.86
According to VolSite

Ligand :

HET Code:	MLD
Formula:	C37H57N7O20
Molecular weight:	919.883 g/mol
DrugBank ID:	DB04736
Buried Surface Area:	57.96 %
Polar Surface area:	429.47 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	10
Rings:	3
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	24

Mass center Coordinates

X	Y	Z
-15.6377	-80.4726	-71.2921

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
OAC	NE2	HIS- 206	2.84	178.58	H-Bond (Protein Donor)	false
NAD	O	THR- 207	3.1	143.43	H-Bond (Ligand Donor)	false
CAF	CB	THR- 207	4.17	0	Hydrophobic	false
CAA	CB	ALA- 208	4	0	Hydrophobic	false
CA5	CB	ALA- 208	4.5	0	Hydrophobic	false
CA3	CB	ALA- 208	4.1	0	Hydrophobic	false
CAJ	CB	ALA- 208	4.44	0	Hydrophobic	false
C6	CD	ARG- 215	3.83	0	Hydrophobic	false
CA1	CG	ARG- 223	3.73	0	Hydrophobic	false
CA6	CG	ARG- 223	3.98	0	Hydrophobic	false
CAF	SD	MET- 225	3.74	0	Hydrophobic	false
CA1	CE2	PHE- 228	4.08	0	Hydrophobic	false
OAG	NE2	HIS- 229	2.66	159.98	H-Bond (Protein Donor)	false
N2	OE2	GLU- 231	2.74	135.5	H-Bond (Ligand Donor)	false
O3	OE1	GLU- 231	2.63	140.68	H-Bond (Ligand Donor)	false
O3	OE2	GLU- 231	3.16	139.23	H-Bond (Ligand Donor)	false
OA6	NH2	ARG- 233	3.03	124.94	H-Bond (Protein Donor)	false
CB	CZ3	TRP- 235	3.86	0	Hydrophobic	false
CBC	CH2	TRP- 235	3.89	0	Hydrophobic	false
CBP	CE2	TRP- 235	4.12	0	Hydrophobic	false
CBR	CB	TRP- 235	4.22	0	Hydrophobic	false
OBU	N	ASN- 236	2.7	168.94	H-Bond (Protein Donor)	false
CB	CB	ALA- 239	4.05	0	Hydrophobic	false
OAM	OH	TYR- 240	2.51	153	H-Bond (Protein Donor)	false
CB	CE2	TYR- 240	4.46	0	Hydrophobic	false
OBV	CZ	ARG- 254	3.73	0	Ionic (Protein Cationic)	false
OBU	CZ	ARG- 254	3.7	0	Ionic (Protein Cationic)	false
OBV	NH1	ARG- 254	3.09	161.63	H-Bond (Protein Donor)	false
OBV	NH2	ARG- 254	3.48	139.48	H-Bond (Protein Donor)	false
OBU	NH2	ARG- 254	2.7	159.38	H-Bond (Protein Donor)	false
CBP	CB	ALA- 261	3.55	0	Hydrophobic	false
NAN	O	HIS- 262	3.12	175.65	H-Bond (Ligand Donor)	false
OBA	N	LEU- 264	3.27	166.32	H-Bond (Protein Donor)	false
CBB	CG	LEU- 264	4.3	0	Hydrophobic	false
OBE	ND2	ASN- 267	2.74	151.93	H-Bond (Protein Donor)	false
OBO	ND2	ASN- 267	3.24	161.15	H-Bond (Protein Donor)	false
CAA	SG	CYS- 278	4.07	0	Hydrophobic	false
CAA	SD	MET- 280	3.92	0	Hydrophobic	false
C4	CB	THR- 320	3.82	0	Hydrophobic	false
CAA	CB	GLU- 321	3.92	0	Hydrophobic	false
O3	N	GLU- 321	3.01	158.22	H-Bond (Protein Donor)	false
CAJ	CB	SER- 322	3.5	0	Hydrophobic	false
OBO	O	HOH- 2040	2.8	179.98	H-Bond (Protein Donor)	false