scPDB - 3b8x entry

Protein Data Bank Entry:

PDB ID : 3b8x

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2007-11-02

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	77 %
B	23 %

Ligand binding site composition:

B-Factor:	17.100
Number of residues:	55
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.613	610.875

% Hydrophobic	% Polar
52.49	47.51
According to VolSite

Ligand :

HET Code:	G4M
Formula:	C24H33N7O19P3
Molecular weight:	816.476 g/mol
DrugBank ID:	-
Buried Surface Area:	64.95 %
Polar Surface area:	444.21 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	8
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
75.082	52.7982	5.66742

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
C4'	CB	ALA- 7	4.23	0	Hydrophobic	false
N1	O	LYS- 26	2.66	163.97	H-Bond (Ligand Donor)	false
N2	O	LYS- 26	3.2	131.4	H-Bond (Ligand Donor)	false
O6	N	PHE- 28	2.81	156.87	H-Bond (Protein Donor)	false
N7	OG1	THR- 29	3.18	149.83	H-Bond (Protein Donor)	false
O6	N	THR- 29	3.34	151.87	H-Bond (Protein Donor)	false
OP2	N	GLY- 56	2.93	152.83	H-Bond (Protein Donor)	false
OP1	N	SER- 57	3.07	138.5	H-Bond (Protein Donor)	false
OP1	OG	SER- 57	2.64	157.39	H-Bond (Protein Donor)	false
C5B	CB	SER- 57	4.17	0	Hydrophobic	false
C2A	CB	TRP- 88	3.64	0	Hydrophobic	false
C5G	CZ3	TRP- 88	3.84	0	Hydrophobic	false
C6G	CE3	TRP- 88	4.25	0	Hydrophobic	false
C2G	CZ2	TRP- 88	3.88	0	Hydrophobic	false
C2A	CG1	VAL- 133	4.16	0	Hydrophobic	false
N1L	OD2	ASP- 159	2.69	177.6	H-Bond (Ligand Donor)	false
N1L	OD1	ASP- 159	3.16	122.52	H-Bond (Ligand Donor)	false
C2A	CB	CYS- 161	4.48	0	Hydrophobic	false
C2A	CG	GLU- 162	3.97	0	Hydrophobic	false
O3L	OE2	GLU- 162	2.78	157.24	H-Bond (Ligand Donor)	false
OP2	OG	SER- 183	2.57	154.44	H-Bond (Protein Donor)	false
C1G	CD2	PHE- 185	4.35	0	Hydrophobic	false
C4'	CD2	TYR- 186	4.49	0	Hydrophobic	false
C1'	CE2	TYR- 186	3.4	0	Hydrophobic	false
DuAr	DuAr	TYR- 186	3.38	0	Aromatic Face/Face	false
O3P	OG	SER- 187	3.34	165.71	H-Bond (Protein Donor)	false
C5'	CB	SER- 187	3.75	0	Hydrophobic	false
O4P	NH2	ARG- 219	2.91	155.94	H-Bond (Protein Donor)	false
O4P	NH1	ARG- 219	3.17	139.75	H-Bond (Protein Donor)	false
O1P	NH1	ARG- 219	2.91	150.31	H-Bond (Protein Donor)	false
O4P	CZ	ARG- 219	3.47	0	Ionic (Protein Cationic)	false
O1P	CZ	ARG- 219	3.89	0	Ionic (Protein Cationic)	false
OP1	ND2	ASN- 248	2.93	161.01	H-Bond (Protein Donor)	false
C6G	CZ	PHE- 302	3.94	0	Hydrophobic	false
O3'	OE2	GLU- 329	3.17	161.1	H-Bond (Ligand Donor)	false
O4P	CZ	ARG- 331	2.79	0	Ionic (Protein Cationic)	false
C6G	CG1	VAL- 334	3.88	0	Hydrophobic	false
OP2	O	HOH- 677	2.74	167.13	H-Bond (Protein Donor)	false