scPDB - 3d8v entry

Protein Data Bank Entry:

PDB ID : 3d8v

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2008-05-25

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:	54.395
Number of residues:	54
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.223	1272.375

% Hydrophobic	% Polar
42.71	57.29
According to VolSite

Ligand :

HET Code:	UD1
Formula:	C17H25N3O17P2
Molecular weight:	605.338 g/mol
DrugBank ID:	DB03397
Buried Surface Area:	62.79 %
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
28.2959	-32.2837	37.3012

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
C1B	CB	LEU- 12	3.8	0	Hydrophobic	false
C4B	CB	LEU- 12	4.22	0	Hydrophobic	false
O2	N	ALA- 14	2.79	139.44	H-Bond (Protein Donor)	false
O2'	N	GLY- 15	2.91	138.71	H-Bond (Protein Donor)	false
N3	OE1	GLN- 83	2.96	171.08	H-Bond (Ligand Donor)	false
O4	NE2	GLN- 83	3.36	133.04	H-Bond (Protein Donor)	false
O4	N	GLY- 88	2.96	139.48	H-Bond (Protein Donor)	false
C8'	CG2	THR- 89	3.22	0	Hydrophobic	false
C5B	CG2	THR- 89	3.99	0	Hydrophobic	false
C4B	CB	SER- 112	4.2	0	Hydrophobic	false
C6'	CD2	TYR- 150	3.84	0	Hydrophobic	false
O4'	N	GLY- 151	3.01	173.98	H-Bond (Protein Donor)	false
N2'	OE1	GLU- 166	2.55	154.03	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 166	3.32	128.95	H-Bond (Ligand Donor)	false
O3'	ND2	ASN- 181	2.88	152.96	H-Bond (Protein Donor)	false
O4'	O	ASN- 181	2.58	170.97	H-Bond (Ligand Donor)	false
C4'	CB	ASN- 181	3.97	0	Hydrophobic	false
C8'	CB	LEU- 210	4.43	0	Hydrophobic	false
C3'	CG2	THR- 211	4.41	0	Hydrophobic	false
C8'	CG2	THR- 211	3.82	0	Hydrophobic	false
O2B	ND2	ASN- 239	3.08	153.45	H-Bond (Protein Donor)	false
O1B	O	HOH- 586	2.77	179.96	H-Bond (Protein Donor)	false