scPDB - 3dj4 entry

Protein Data Bank Entry:

PDB ID : 3dj4

Resolution :2.380 Å

Experimental Method : X-ray

Deposition Date : 2008-06-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Bifunctional protein GlmU
ID:	GLMU_MYCTU
AC:	P9WMN3
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.274
Number of residues:	51
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.341	853.875

% Hydrophobic	% Polar
35.18	64.82
According to VolSite

Ligand :

HET Code:	UD1
Formula:	C17H25N3O17P2
Molecular weight:	605.338 g/mol
DrugBank ID:	DB03397
Buried Surface Area:	67.97 %
Polar Surface area:	325.69 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
12.1365	32.3468	39.7145

Binding mode :

What is Poseview ?

2D View
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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
C1B	CB	LEU- 12	3.76	0	Hydrophobic	false
C4B	CB	LEU- 12	4.42	0	Hydrophobic	false
O3B	O	LEU- 12	2.89	168.71	H-Bond (Ligand Donor)	false
O2	N	ALA- 14	2.9	137.44	H-Bond (Protein Donor)	false
O2'	N	GLY- 15	3.1	151.44	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 26	3.12	0	Ionic (Protein Cationic)	false
O4	N	GLY- 88	3.12	139.14	H-Bond (Protein Donor)	false
C8'	CG2	THR- 89	4.5	0	Hydrophobic	false
C1B	CG2	THR- 89	4.48	0	Hydrophobic	false
C5B	CG2	THR- 89	3.62	0	Hydrophobic	false
O7'	OG1	THR- 89	2.74	168	H-Bond (Protein Donor)	false
C4B	CB	SER- 112	3.77	0	Hydrophobic	false
O3B	N	GLY- 113	3.32	130.81	H-Bond (Protein Donor)	false
C6'	CD1	TYR- 150	3.75	0	Hydrophobic	false
O4'	N	GLY- 151	3.03	166.64	H-Bond (Protein Donor)	false
C8'	CG	GLU- 166	4.06	0	Hydrophobic	false
N2'	OE1	GLU- 166	2.89	151.54	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 166	3.49	136.16	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 166	3.07	161.68	H-Bond (Ligand Donor)	false
C4'	CB	ASN- 181	4.06	0	Hydrophobic	false
O3'	ND2	ASN- 181	2.7	146.58	H-Bond (Protein Donor)	false
O4'	O	ASN- 181	2.69	167.42	H-Bond (Ligand Donor)	false
C8'	CD1	TYR- 209	3.85	0	Hydrophobic	false
C8'	CG2	THR- 211	4.04	0	Hydrophobic	false
O1B	ND2	ASN- 239	3.21	136.73	H-Bond (Protein Donor)	false
O2A	MG	MG- 496	2.09	0	Metal Acceptor	false
O1B	MG	MG- 496	1.98	0	Metal Acceptor	false