scPDB - 1lmc entry

Protein Data Bank Entry:

PDB ID : 1lmc

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1994-11-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lysozyme C II
ID:	LYSC2_ONCMY
AC:	P11941
Organism:	Oncorhynchus mykiss
Reign:	Eukaryota
TaxID:	8022
EC Number:	3.2.1.17

Chains:

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

Ligand binding site composition:

B-Factor:	27.609
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.107	327.375

% Hydrophobic	% Polar
44.33	55.67
According to VolSite

Ligand :

HET Code:	BUL
Formula:	C16H28N3O14S2
Molecular weight:	550.535 g/mol
DrugBank ID:	-
Buried Surface Area:	49.18 %
Polar Surface area:	294.34 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	6
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
44.5174	42.6091	27.3161

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
O22	OE2	GLU- 35	2.81	164.32	H-Bond (Ligand Donor)	false
C27	CB	ASN- 46	4.36	0	Hydrophobic	false
O31	ND2	ASN- 46	2.69	135.4	H-Bond (Protein Donor)	false
O30	N	THR- 47	2.76	136.78	H-Bond (Protein Donor)	false
O30	OG1	THR- 47	2.51	155.47	H-Bond (Protein Donor)	false
N7	OD2	ASP- 52	2.88	164.19	H-Bond (Ligand Donor)	false
N7	OD2	ASP- 52	2.88	0	Ionic (Ligand Cationic)	false
N7	OD1	ASP- 52	3.68	0	Ionic (Ligand Cationic)	false
C21	CB	GLN- 57	4.44	0	Hydrophobic	false
C19	CG1	ILE- 58	4.3	0	Hydrophobic	false
C2	CB	ASN- 59	4.33	0	Hydrophobic	false
C10	CB	ASN- 59	4.31	0	Hydrophobic	false
O18	N	ASN- 59	2.83	162.26	H-Bond (Protein Donor)	false
C12	CE2	TYR- 62	3.64	0	Hydrophobic	false
O15	NE1	TRP- 63	2.87	164.99	H-Bond (Protein Donor)	false
C19	CG1	VAL- 98	4.31	0	Hydrophobic	false
C4	CB	ALA- 107	3.98	0	Hydrophobic	false
N16	O	ALA- 107	3.17	141	H-Bond (Ligand Donor)	false
C19	CE2	TRP- 108	3.28	0	Hydrophobic	false
O22	N	VAL- 109	3.01	155.24	H-Bond (Protein Donor)	false
C10	CG2	VAL- 109	4.3	0	Hydrophobic	false