scPDB - 2gmu entry

Protein Data Bank Entry:

PDB ID : 2gmu

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2006-04-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative pyridoxamine 5-phosphate-dependent dehydrase
ID:	Q9F118_ECOLX
AC:	Q9F118
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	562
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	14 %
B	86 %

Ligand binding site composition:

B-Factor:	35.056
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.129	651.375

% Hydrophobic	% Polar
48.70	51.30
According to VolSite

Ligand :

HET Code:	PDG
Formula:	C13H16N2O9P
Molecular weight:	375.248 g/mol
DrugBank ID:	DB04762
Buried Surface Area:	74.01 %
Polar Surface area:	212.22 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
17.8363	10.1647	20.9789

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
OP2	N	GLY- 56	2.76	158.45	H-Bond (Protein Donor)	false
OP3	N	SER- 57	2.99	136.84	H-Bond (Protein Donor)	false
C2A	CB	TRP- 88	3.56	0	Hydrophobic	false
CBA	CE2	TRP- 88	3.31	0	Hydrophobic	false
CGA	CZ2	TRP- 88	4.13	0	Hydrophobic	false
C4	CB	TRP- 88	3.68	0	Hydrophobic	false
C2A	CG1	VAL- 133	4.17	0	Hydrophobic	false
N1	OD2	ASP- 159	2.67	149.96	H-Bond (Ligand Donor)	false
C2A	CB	CYS- 161	4.5	0	Hydrophobic	false
C5	CB	CYS- 161	3.8	0	Hydrophobic	false
C2A	CG	GLU- 162	4.27	0	Hydrophobic	false
C3	CG	GLU- 162	4.13	0	Hydrophobic	false
O3	OE2	GLU- 162	2.7	141.19	H-Bond (Ligand Donor)	false
C5A	CB	SER- 183	4.44	0	Hydrophobic	false
OP2	OG	SER- 183	2.97	160.01	H-Bond (Protein Donor)	false
CGA	CE2	PHE- 185	4.02	0	Hydrophobic	false
OXT	NE2	HIS- 188	2.72	165.39	H-Bond (Protein Donor)	false
OP3	ND2	ASN- 248	3.04	168.14	H-Bond (Protein Donor)	false
OE1	NH2	ARG- 250	3.22	146.4	H-Bond (Protein Donor)	false
OE2	NH2	ARG- 250	3.43	133.41	H-Bond (Protein Donor)	false
OE2	NH1	ARG- 250	2.83	170.51	H-Bond (Protein Donor)	false
OE1	CZ	ARG- 250	3.96	0	Ionic (Protein Cationic)	false
OE2	CZ	ARG- 250	3.58	0	Ionic (Protein Cationic)	false
OP2	O	HOH- 523	2.74	179.95	H-Bond (Protein Donor)	false