scPDB - 4d7e entry

Protein Data Bank Entry:

PDB ID : 4d7e

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2014-11-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative lysine-N-oxygenase
ID:	Q5Z1T5_NOCFA
AC:	Q5Z1T5
Organism:	Nocardia farcinica
Reign:	Bacteria
TaxID:	247156
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	48.044
Number of residues:	58
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.423	2173.500

% Hydrophobic	% Polar
43.01	56.99
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	68.23 %
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
66.6367	35.5988	48.9998

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
C5'	CG	PRO- 11	3.71	0	Hydrophobic	false
O1P	N	LYS- 12	2.91	162.15	H-Bond (Protein Donor)	false
O2P	NZ	LYS- 12	2.56	154.48	H-Bond (Protein Donor)	false
O2P	NZ	LYS- 12	2.56	0	Ionic (Protein Cationic)	false
O3B	OE2	GLU- 37	3.14	127.62	H-Bond (Ligand Donor)	false
O3B	OE1	GLU- 37	2.74	172.32	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 37	3.27	151.69	H-Bond (Ligand Donor)	false
N3A	N	ALA- 38	3.03	137.69	H-Bond (Protein Donor)	false
O1A	ND2	ASN- 44	2.52	159.83	H-Bond (Protein Donor)	false
C3B	CB	ASN- 44	4.15	0	Hydrophobic	false
O2A	NE1	TRP- 45	3.24	137.12	H-Bond (Protein Donor)	false
C4'	CZ2	TRP- 45	3.91	0	Hydrophobic	false
C7M	CB	TRP- 51	4.43	0	Hydrophobic	false
C8M	CE3	TRP- 51	3.98	0	Hydrophobic	false
C7M	CB	THR- 52	4.39	0	Hydrophobic	false
O4	N	GLY- 59	3.11	143.12	H-Bond (Protein Donor)	false
N3	OG1	THR- 60	2.79	146.87	H-Bond (Ligand Donor)	false
O4	N	THR- 60	3.46	134.55	H-Bond (Protein Donor)	false
N6A	O	VAL- 137	2.97	162.64	H-Bond (Ligand Donor)	false
N1A	N	VAL- 137	3.02	152.52	H-Bond (Protein Donor)	false
O2P	N	GLY- 174	3.13	145.61	H-Bond (Protein Donor)	false
C6	CB	GLU- 216	3.5	0	Hydrophobic	false
C1'	CB	ASN- 400	4.37	0	Hydrophobic	false
C3'	CB	ASN- 400	4.34	0	Hydrophobic	false
O2	N	LEU- 401	2.78	158.47	H-Bond (Protein Donor)	false
C4'	CD2	LEU- 401	4.38	0	Hydrophobic	false
N5	O	HOH- 2019	3.22	179.97	H-Bond (Protein Donor)	false