scPDB - 5dkk entry

Protein Data Bank Entry:

PDB ID : 5dkk

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2015-09-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Predicted protein
ID:	B7G9J2_PHATC
AC:	B7G9J2
Organism:	Phaeodactylum tricornutum
Reign:	Eukaryota
TaxID:	556484
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.604
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.418	398.250

% Hydrophobic	% Polar
53.39	46.61
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	82.05 %
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
-13.9517	47.5911	-17.0084

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
C6	CG2	VAL- 253	3.42	0	Hydrophobic	false
C7M	CG2	THR- 255	3.53	0	Hydrophobic	false
O3'	ND2	ASN- 286	3.28	141.56	H-Bond (Protein Donor)	false
C6	SG	CYS- 287	4.18	0	Hydrophobic	false
C9A	CB	CYS- 287	3.46	0	Hydrophobic	false
C2'	CB	CYS- 287	3.59	0	Hydrophobic	false
O2'	N	CYS- 287	3.03	122.49	H-Bond (Protein Donor)	false
C2'	CB	ARG- 288	4.21	0	Hydrophobic	false
O2	NE2	GLN- 291	2.73	168.53	H-Bond (Protein Donor)	false
C1'	CG2	ILE- 303	4.4	0	Hydrophobic	false
O3P	CZ	ARG- 304	3.27	0	Ionic (Protein Cationic)	false
C5'	CD1	ILE- 307	3.92	0	Hydrophobic	false
C8M	CD1	ILE- 307	3.73	0	Hydrophobic	false
O2	ND2	ASN- 319	3.23	154.99	H-Bond (Protein Donor)	false
N3	OD1	ASN- 319	3	140.71	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 329	3.28	121.61	H-Bond (Protein Donor)	false
C7	CD1	ILE- 333	3.85	0	Hydrophobic	false
C8	CD1	ILE- 333	3.44	0	Hydrophobic	false
C7M	CB	PHE- 346	3.69	0	Hydrophobic	false
C8M	CB	PHE- 346	3.67	0	Hydrophobic	false
O4	NE2	GLN- 350	2.64	159.4	H-Bond (Protein Donor)	false
O3'	O	HOH- 601	3.45	168.31	H-Bond (Protein Donor)	false