scPDB - 2f1k entry

Protein Data Bank Entry:

PDB ID : 2f1k

Resolution :1.550 Å

Experimental Method : X-ray

Deposition Date : 2005-11-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Prephenate dehydrogenase
ID:	P73906_SYNY3
AC:	P73906
Organism:	Synechocystis sp.
Reign:	Bacteria
TaxID:	1111708
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.117
Number of residues:	46
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.410	2153.250

% Hydrophobic	% Polar
41.69	58.31
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	61.26 %
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
26.9215	13.7013	25.5604

Binding mode :

What is Poseview ?

2D View
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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
O2A	N	LEU- 10	2.89	172.83	H-Bond (Protein Donor)	false
O2N	N	ILE- 11	2.93	172.89	H-Bond (Protein Donor)	false
C3N	CG1	ILE- 11	3.64	0	Hydrophobic	false
C4N	CD1	ILE- 11	3.79	0	Hydrophobic	false
C5N	CG1	ILE- 11	4.14	0	Hydrophobic	false
O2X	OG	SER- 30	2.66	143.29	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 31	2.6	142.04	H-Bond (Protein Donor)	false
O3X	NE	ARG- 31	2.85	134.28	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 31	3.12	0	Ionic (Protein Cationic)	false
O2X	N	GLN- 32	2.88	167.3	H-Bond (Protein Donor)	false
O3X	NE2	GLN- 32	3	171.1	H-Bond (Protein Donor)	false
O1X	OG1	THR- 35	2.52	168.18	H-Bond (Protein Donor)	false
O3D	O	THR- 65	2.88	154.26	H-Bond (Ligand Donor)	false
C5B	CG	PRO- 66	4.4	0	Hydrophobic	false
C3D	CG1	ILE- 67	4.23	0	Hydrophobic	false
C4D	CG2	VAL- 90	3.99	0	Hydrophobic	false
O2D	N	SER- 92	3.14	146.88	H-Bond (Protein Donor)	false
C5N	CG	PRO- 113	4.35	0	Hydrophobic	false
O1A	NE2	GLN- 120	2.83	173.98	H-Bond (Protein Donor)	false
O2A	N	GLY- 121	2.8	165.49	H-Bond (Protein Donor)	false
O2N	O	HOH- 2355	2.8	179.97	H-Bond (Protein Donor)	false