scPDB - 3m9v entry

Protein Data Bank Entry:

PDB ID : 3m9v

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2010-03-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	FAD-dependent oxidoreductase
ID:	B3TMR1_9ACTN
AC:	B3TMR1
Organism:	Actinomadura kijaniata
Reign:	Bacteria
TaxID:	46161
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.463
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.099	1350.000

% Hydrophobic	% Polar
42.75	57.25
According to VolSite

Ligand :

HET Code:	TYD
Formula:	C10H13N2O11P2
Molecular weight:	399.165 g/mol
DrugBank ID:	DB03103
Buried Surface Area:	52.76 %
Polar Surface area:	220.27 Å2

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

Mass center Coordinates

X	Y	Z
19.8698	26.6481	-14.5152

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
C1'	CB	THR- 109	3.53	0	Hydrophobic	false
C5M	CZ	TYR- 112	4.23	0	Hydrophobic	false
C2'	CD2	TYR- 112	3.76	0	Hydrophobic	false
O3'	OE1	GLU- 113	2.97	145.59	H-Bond (Ligand Donor)	false
C2'	CG	GLU- 113	4.16	0	Hydrophobic	false
O1B	ND2	ASN- 182	3.36	136.18	H-Bond (Protein Donor)	false
C5M	CB	ALA- 252	4.4	0	Hydrophobic	false
O2B	NE2	GLN- 254	2.9	163.69	H-Bond (Protein Donor)	false
O2A	OG	SER- 257	2.73	164.18	H-Bond (Protein Donor)	false
O4	NH1	ARG- 330	3.18	134.46	H-Bond (Protein Donor)	false
O4	NH2	ARG- 330	2.73	161.04	H-Bond (Protein Donor)	false