scPDB - 5dp2 entry

Protein Data Bank Entry:

PDB ID : 5dp2

Resolution :0.960 Å

Experimental Method : X-ray

Deposition Date : 2015-09-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	CurF
ID:	Q6DNE7_9CYAN
AC:	Q6DNE7
Organism:	Lyngbya majuscula
Reign:	Bacteria
TaxID:	158786
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	8.261
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.185	985.500

% Hydrophobic	% Polar
47.95	52.05
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	63.94 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-0.0270417	25.0447	-20.7247

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
C5B	CD1	PHE- 45	3.82	0	Hydrophobic	false
C3D	CD2	PHE- 45	3.63	0	Hydrophobic	false
O1N	N	PHE- 45	2.95	170.31	H-Bond (Protein Donor)	false
C4N	SD	MET- 136	4.49	0	Hydrophobic	false
C5N	CG	MET- 136	4.31	0	Hydrophobic	false
C4N	CG2	THR- 140	3.72	0	Hydrophobic	false
C1B	CB	ALA- 161	3.8	0	Hydrophobic	false
O1X	OG	SER- 163	2.64	167.29	H-Bond (Protein Donor)	false
O1A	N	GLY- 165	2.91	159.44	H-Bond (Protein Donor)	false
O2N	N	ALA- 166	2.92	158.59	H-Bond (Protein Donor)	false
C5D	CB	ALA- 166	4.13	0	Hydrophobic	false
O2X	N	SER- 186	3	139.15	H-Bond (Protein Donor)	false
O2X	OG	SER- 186	2.65	153.93	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 189	2.74	162.42	H-Bond (Protein Donor)	false
O3X	NZ	LYS- 189	3.43	132.3	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 189	2.74	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 189	3.43	0	Ionic (Protein Cationic)	false
O3X	NH2	ARG- 205	3.02	147.17	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 205	3.48	171.89	Pi/Cation	false
C4D	CB	SER- 228	3.57	0	Hydrophobic	false
C1B	CD2	LEU- 229	4.21	0	Hydrophobic	false
C4D	CD1	ILE- 251	4.28	0	Hydrophobic	false
C3N	CB	ILE- 251	4.05	0	Hydrophobic	false
N7N	O	ILE- 251	2.9	172.32	H-Bond (Ligand Donor)	false
N7N	O	PHE- 274	2.84	150.64	H-Bond (Ligand Donor)	false
O7N	N	MET- 276	2.72	174.83	H-Bond (Protein Donor)	false
O3X	OG	SER- 326	2.57	171.37	H-Bond (Protein Donor)	false
O1A	NE2	HIS- 328	2.85	159.16	H-Bond (Protein Donor)	false
O2A	O	HOH- 576	2.69	179.95	H-Bond (Protein Donor)	false
O2D	O	HOH- 780	2.87	164.56	H-Bond (Ligand Donor)	false