scPDB - 4obu entry

Protein Data Bank Entry:

PDB ID : 4obu

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2014-01-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyridoxal-dependent decarboxylase domain protein
ID:	A7B1V0_RUMGN
AC:	A7B1V0
Organism:	Ruminococcus gnavus ATCC 29149
Reign:	Bacteria
TaxID:	411470
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	82 %
C	18 %

Ligand binding site composition:

B-Factor:	14.150
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.874	519.750

% Hydrophobic	% Polar
51.95	48.05
According to VolSite

Ligand :

HET Code:	PLP
Formula:	C8H8NO6P
Molecular weight:	245.126 g/mol
DrugBank ID:	DB00114
Buried Surface Area:	73.51 %
Polar Surface area:	132.42 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
21.1917	103.222	84.9391

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
O2P	N	GLY- 159	3.48	151.85	H-Bond (Protein Donor)	false
O1P	OG	SER- 160	2.62	167.63	H-Bond (Protein Donor)	false
O1P	N	SER- 160	3.36	146.73	H-Bond (Protein Donor)	false
C2A	CB	HIS- 192	4.3	0	Hydrophobic	false
C3	CB	HIS- 192	4.49	0	Hydrophobic	false
DuAr	DuAr	HIS- 192	3.87	0	Aromatic Face/Face	false
C2A	CG2	THR- 245	4.2	0	Hydrophobic	false
O3	OG1	THR- 249	3.07	138.26	H-Bond (Protein Donor)	false
N1	OD1	ASP- 274	2.93	125.3	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 274	2.59	164.03	H-Bond (Ligand Donor)	false
C2A	CB	ALA- 276	4.21	0	Hydrophobic	false
C5	CB	ALA- 276	3.63	0	Hydrophobic	false
O2P	NZ	LYS- 306	3.75	0	Ionic (Protein Cationic)	false
O2P	OH	TYR- 312	2.84	138.69	H-Bond (Protein Donor)	false
O3P	OG1	THR- 356	2.93	145.1	H-Bond (Protein Donor)	false
O3P	N	THR- 356	3.37	144.43	H-Bond (Protein Donor)	false