scPDB - 4xg1 entry

Protein Data Bank Entry:

PDB ID : 4xg1

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2014-12-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Diaminopimelate decarboxylase
ID:	A1SR00_PSYIN
AC:	A1SR00
Organism:	Psychromonas ingrahamii
Reign:	Bacteria
TaxID:	357804
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	90 %
D	10 %

Ligand binding site composition:

B-Factor:	18.925
Number of residues:	46
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.712	887.625

% Hydrophobic	% Polar
40.68	59.32
According to VolSite

Ligand :

HET Code:	LLP
Formula:	C14H20N3O7P
Molecular weight:	373.298 g/mol
DrugBank ID:	DB04083
Buried Surface Area:	76.06 %
Polar Surface area:	195.48 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
58.7467	4.76212	27.8432

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
C5'	CB	ALA- 59	3.64	0	Hydrophobic	false
C4	CD	LYS- 61	3.78	0	Hydrophobic	false
C2'	CB	SER- 103	3.99	0	Hydrophobic	false
C2'	CB	HIS- 200	3.77	0	Hydrophobic	false
DuAr	DuAr	HIS- 200	3.52	0	Aromatic Face/Face	false
CD	CB	SER- 203	4.28	0	Hydrophobic	false
OP2	N	GLY- 240	3.05	162.51	H-Bond (Protein Donor)	false
OP2	N	GLY- 276	2.86	150.92	H-Bond (Protein Donor)	false
OP3	N	ARG- 277	2.89	159.58	H-Bond (Protein Donor)	false
OXT	CZ	ARG- 277	3.36	0	Ionic (Protein Cationic)	false
O	NE	ARG- 313	2.76	175.28	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 313	2.91	155.45	H-Bond (Protein Donor)	false
O	CZ	ARG- 313	3.58	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 313	3.7	0	Ionic (Protein Cationic)	false
N	OH	TYR- 317	2.85	146.31	H-Bond (Ligand Donor)	false
N	OE1	GLU- 349	3.94	0	Ionic (Ligand Cationic)	false
CG	CG	GLU- 349	3.28	0	Hydrophobic	false
OP3	OH	TYR- 376	2.56	179.2	H-Bond (Protein Donor)	false
CD	CZ	TYR- 376	3.83	0	Hydrophobic	false
CB	CE1	TYR- 376	3.84	0	Hydrophobic	false
N	OH	TYR- 384	3.17	146.73	H-Bond (Ligand Donor)	false
OP2	O	HOH- 628	2.63	150.31	H-Bond (Protein Donor)	false
OP1	O	HOH- 658	2.62	179.95	H-Bond (Protein Donor)	false