scPDB - 4j8p entry

Protein Data Bank Entry:

PDB ID : 4j8p

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2013-02-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Flavodoxin
ID:	A7VAB4_BACUC
AC:	A7VAB4
Organism:	Bacteroides uniformis
Reign:	Bacteria
TaxID:	411479
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.497
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.226	401.625

% Hydrophobic	% Polar
29.41	70.59
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	73.54 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
25.7669	2.921	14.3066

Binding mode :

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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
O2P	OG	SER- 33	2.65	146.41	H-Bond (Protein Donor)	false
O1P	N	ALA- 34	2.82	141.45	H-Bond (Protein Donor)	false
O1P	N	THR- 35	3.07	155.08	H-Bond (Protein Donor)	false
O3P	N	THR- 35	3.22	128.6	H-Bond (Protein Donor)	false
O3P	OG1	THR- 35	2.58	167.48	H-Bond (Protein Donor)	false
C5'	CB	THR- 37	4.29	0	Hydrophobic	false
O3P	N	THR- 37	2.87	159.03	H-Bond (Protein Donor)	false
O3P	OG1	THR- 37	3.02	146.31	H-Bond (Protein Donor)	false
O2P	OG1	THR- 38	2.76	148.18	H-Bond (Protein Donor)	false
O2P	N	THR- 38	2.74	164.8	H-Bond (Protein Donor)	false
C8M	CD2	LEU- 67	3.85	0	Hydrophobic	false
C7	CB	TRP- 69	4.26	0	Hydrophobic	false
C7M	CB	SER- 76	3.64	0	Hydrophobic	false
C2'	CB	PRO- 107	4.35	0	Hydrophobic	false
C5'	CB	PRO- 107	3.67	0	Hydrophobic	false
O2'	O	ILE- 108	2.66	161.09	H-Bond (Ligand Donor)	false
C7M	CD2	TRP- 109	3.98	0	Hydrophobic	false
C8M	CE2	TRP- 109	4.01	0	Hydrophobic	false
C6	CB	TRP- 109	3.88	0	Hydrophobic	false
N5	N	TRP- 110	2.82	165.64	H-Bond (Protein Donor)	false
O4	N	ASN- 111	2.92	132.2	H-Bond (Protein Donor)	false
C4'	CB	THR- 136	4.48	0	Hydrophobic	false
O4'	OG1	THR- 136	2.78	167.76	H-Bond (Protein Donor)	false
N1	N	GLY- 138	3.05	162.55	H-Bond (Protein Donor)	false
O2	N	SER- 139	2.77	159.16	H-Bond (Protein Donor)	false
O2	N	SER- 140	2.8	176.91	H-Bond (Protein Donor)	false
N3	OG	SER- 140	2.85	160.43	H-Bond (Ligand Donor)	false