scPDB - 4ybn entry

Protein Data Bank Entry:

PDB ID : 4ybn

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2015-02-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Flavin-nucleotide-binding protein
ID:	A0R238_MYCS2
AC:	A0R238
Organism:	Mycobacterium smegmatis 155)
Reign:	Bacteria
TaxID:	246196
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	55 %
B	45 %

Ligand binding site composition:

B-Factor:	32.504
Number of residues:	50
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.308	2291.625

% Hydrophobic	% Polar
44.92	55.08
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	79.8 %
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
20.133	-0.381642	14.506

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
C1B	CG2	VAL- 12	3.76	0	Hydrophobic	false
O1A	OG1	THR- 13	2.51	166.26	H-Bond (Protein Donor)	false
O1P	N	THR- 13	2.93	126.59	H-Bond (Protein Donor)	false
C5'	CB	ARG- 14	3.84	0	Hydrophobic	false
O1P	N	ARG- 14	2.8	162.07	H-Bond (Protein Donor)	false
C7M	CD2	LEU- 35	3.28	0	Hydrophobic	false
C3B	CE2	PHE- 49	4.06	0	Hydrophobic	false
C3'	CD2	PHE- 49	4.46	0	Hydrophobic	false
C7	CB	PRO- 50	4.39	0	Hydrophobic	false
C8M	CG	PRO- 50	3.51	0	Hydrophobic	false
C9	CG	PRO- 50	3.64	0	Hydrophobic	false
O2'	O	PRO- 50	2.69	159.64	H-Bond (Ligand Donor)	false
O4	N	GLY- 52	3.35	139.59	H-Bond (Protein Donor)	false
N5	N	GLY- 52	2.9	143.6	H-Bond (Protein Donor)	false
N3	O	HIS- 63	2.73	141.12	H-Bond (Ligand Donor)	false
O2P	OG	SER- 68	2.98	139.51	H-Bond (Protein Donor)	false
C2'	CZ2	TRP- 70	4.3	0	Hydrophobic	false
C4'	CE2	TRP- 70	4.39	0	Hydrophobic	false
O4'	NE1	TRP- 70	2.73	133.43	H-Bond (Protein Donor)	false
O5'	NE1	TRP- 70	3.07	129.23	H-Bond (Protein Donor)	false
C7M	CG2	THR- 85	4.07	0	Hydrophobic	false
C8M	CG2	THR- 85	3.84	0	Hydrophobic	false
C7M	CD1	LEU- 87	4.11	0	Hydrophobic	false
C8M	CE1	TYR- 103	3.23	0	Hydrophobic	false
C1'	CZ	TYR- 103	4.37	0	Hydrophobic	false
C7M	CB	TYR- 103	3.48	0	Hydrophobic	false
DuAr	DuAr	TYR- 103	3.91	0	Aromatic Face/Face	false
C8M	CB	SER- 105	3.56	0	Hydrophobic	false
N3A	OG1	THR- 107	3.35	164.84	H-Bond (Protein Donor)	false
O2B	OG	SER- 163	2.64	164.56	H-Bond (Ligand Donor)	false
C1B	CB	SER- 163	3.9	0	Hydrophobic	false
O3'	NZ	LYS- 165	2.81	153.13	H-Bond (Protein Donor)	false