scPDB - 2k5t entry

Protein Data Bank Entry:

PDB ID : 2k5t

Resolution : Å

Experimental Method : NMR

Deposition Date : 2008-06-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	PanD regulatory factor
ID:	PANM_ECOLI
AC:	P37613
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	0.000
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.172	793.125

% Hydrophobic	% Polar
55.74	44.26
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	51.36 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
87.2599	-1.35648	-1.90981

Binding mode :

What is Poseview ?

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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
S1P	CB	SER- 65	4.18	0	Hydrophobic	false
C6P	CG	ARG- 67	3.51	0	Hydrophobic	false
C2P	CG	ARG- 67	3.85	0	Hydrophobic	false
O5P	NE	ARG- 67	2.65	165.46	H-Bond (Protein Donor)	false
CEP	CG2	VAL- 68	3.72	0	Hydrophobic	false
CAP	CB	VAL- 68	3.72	0	Hydrophobic	false
O9P	N	VAL- 68	2.69	157.04	H-Bond (Protein Donor)	false
CCP	CG	ARG- 73	4.29	0	Hydrophobic	false
C5B	CG	ARG- 74	4.07	0	Hydrophobic	false
O2A	N	ARG- 75	2.85	159.19	H-Bond (Protein Donor)	false
O4A	N	ARG- 75	3.45	123.64	H-Bond (Protein Donor)	false
O2A	N	GLY- 76	2.98	135.43	H-Bond (Protein Donor)	false
O5A	N	GLY- 78	2.76	124.73	H-Bond (Protein Donor)	false
O2B	OE1	GLN- 79	3.01	164.12	H-Bond (Ligand Donor)	false
C4B	CG	GLN- 79	4.29	0	Hydrophobic	false
O1A	N	GLN- 79	2.75	153.75	H-Bond (Protein Donor)	false
S1P	CG2	VAL- 102	3.23	0	Hydrophobic	false
CDP	CG1	VAL- 107	4.04	0	Hydrophobic	false
CDP	SD	MET- 108	4.12	0	Hydrophobic	false
C1B	CB	PHE- 111	4.41	0	Hydrophobic	false
C2B	CB	ALA- 114	3.7	0	Hydrophobic	false