scPDB - 3c4a entry

Protein Data Bank Entry:

PDB ID : 3c4a

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2008-01-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protodeoxyviolaceinate monooxygenase
ID:	VIOD_CHRVO
AC:	Q9S3U8
Organism:	Chromobacterium violaceum
Reign:	Bacteria
TaxID:	243365
EC Number:	1

Chains:

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

Ligand binding site composition:

B-Factor:	21.723
Number of residues:	65
Including
Standard Amino Acids:	60
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.485	1954.125

% Hydrophobic	% Polar
48.36	51.64
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	68.45 %
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
16.7022	44.9202	35.0501

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
O1P	N	ALA- 11	3.07	148.32	H-Bond (Protein Donor)	false
O3B	OE2	GLU- 32	2.97	154.17	H-Bond (Ligand Donor)	false
C1B	CB	LYS- 33	4.33	0	Hydrophobic	false
N3	O	VAL- 45	3.26	149.88	H-Bond (Ligand Donor)	false
O4	N	VAL- 45	3.04	167.27	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 97	3.44	145.47	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 97	3.24	157.38	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 97	3.8	0	Ionic (Protein Cationic)	false
N6A	O	LEU- 121	3.42	157.59	H-Bond (Ligand Donor)	false
N1A	N	LEU- 121	3.44	168.61	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 142	2.6	163.03	H-Bond (Ligand Donor)	false
C7M	CE2	TYR- 163	3.32	0	Hydrophobic	false
C8M	CZ	TYR- 163	4.11	0	Hydrophobic	false
C7M	CE3	TRP- 165	3.73	0	Hydrophobic	false
C8M	CE3	TRP- 165	4.16	0	Hydrophobic	false
DuAr	DuAr	TRP- 165	3.87	0	Aromatic Face/Face	false
C6	CD1	ILE- 202	3.67	0	Hydrophobic	false
C8M	CE2	PHE- 251	4.37	0	Hydrophobic	false
O3'	OD1	ASP- 269	2.75	157.57	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 269	3.9	0	Hydrophobic	false
O2P	N	ASP- 269	3.29	149.69	H-Bond (Protein Donor)	false
C7M	CD2	PHE- 276	3.67	0	Hydrophobic	false
C6	CB	PHE- 276	3.58	0	Hydrophobic	false
O2	N	THR- 282	2.93	159.96	H-Bond (Protein Donor)	false
O2	OG1	THR- 282	2.97	147.39	H-Bond (Protein Donor)	false
O4'	OG1	THR- 282	3.49	133.23	H-Bond (Ligand Donor)	false
O1P	O	HOH- 403	2.76	166.71	H-Bond (Protein Donor)	false
O2P	O	HOH- 404	2.91	179.96	H-Bond (Protein Donor)	false