scPDB - 3lcm entry

Protein Data Bank Entry:

PDB ID : 3lcm

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2010-01-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative oxidoreductase
ID:	Q8DTD1_STRMU
AC:	Q8DTD1
Organism:	Streptococcus mutans serotype c
Reign:	Bacteria
TaxID:	210007
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	70 %
B	30 %

Ligand binding site composition:

B-Factor:	20.180
Number of residues:	47
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.958	948.375

% Hydrophobic	% Polar
45.91	54.09
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	57.91 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
30.5365	5.24192	22.9476

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
O2P	NE2	HIS- 9	2.75	140.99	H-Bond (Protein Donor)	false
O2A	N	PHE- 15	3.31	149.91	H-Bond (Protein Donor)	false
C5B	CB	PHE- 15	4.03	0	Hydrophobic	false
C1B	CD1	PHE- 15	4.35	0	Hydrophobic	false
O1P	N	ASN- 16	2.98	162.61	H-Bond (Protein Donor)	false
O1P	ND2	ASN- 16	2.86	157.75	H-Bond (Protein Donor)	false
C7M	CD2	LEU- 47	3.57	0	Hydrophobic	false
C8M	CD2	LEU- 47	4.28	0	Hydrophobic	false
C8M	CE2	PHE- 49	4.21	0	Hydrophobic	false
C8M	CD	ARG- 55	3.52	0	Hydrophobic	false
C4'	CB	PRO- 82	3.8	0	Hydrophobic	false
O2'	O	ILE- 83	2.63	165.61	H-Bond (Ligand Donor)	false
C7M	CD2	TRP- 84	4.07	0	Hydrophobic	false
C8M	CE2	TRP- 84	4.08	0	Hydrophobic	false
C6	CB	TRP- 84	3.54	0	Hydrophobic	false
N5	N	TRP- 85	2.71	168.01	H-Bond (Protein Donor)	false
O4	N	SER- 86	2.67	146.34	H-Bond (Protein Donor)	false
O4'	OG1	THR- 127	2.81	164.95	H-Bond (Protein Donor)	false
C4'	CB	THR- 127	4.43	0	Hydrophobic	false
O2	N	ASN- 129	2.69	133.9	H-Bond (Protein Donor)	false
O2	OG1	THR- 130	2.66	149.71	H-Bond (Ligand Donor)	false
N3	OH	TYR- 141	2.83	141.87	H-Bond (Ligand Donor)	false
C5'	CG2	ILE- 166	3.87	0	Hydrophobic	false
C4B	CD	ARG- 174	3.94	0	Hydrophobic	false
C1B	CD	ARG- 174	3.81	0	Hydrophobic	false
N3A	NE	ARG- 174	3.24	148.43	H-Bond (Protein Donor)	false