scPDB - 2vd4 entry

Protein Data Bank Entry:

PDB ID : 2vd4

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2007-09-28

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_HAEIN
AC:	P43889
Organism:	Haemophilus influenzae
Reign:	Bacteria
TaxID:	71421
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.642
Number of residues:	24
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.809	465.750

% Hydrophobic	% Polar
39.86	60.14
According to VolSite

Ligand :

HET Code:	P21
Formula:	C24H32ClN2O2
Molecular weight:	415.976 g/mol
DrugBank ID:	DB08344
Buried Surface Area:	42.05 %
Polar Surface area:	33.98 Å2

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

Mass center Coordinates

X	Y	Z
71.0573	30.7375	39.7673

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
C24	CG1	VAL- 131	4.09	0	Hydrophobic	false
C16	CD2	LEU- 133	4.07	0	Hydrophobic	false
C24	CD1	LEU- 133	4.24	0	Hydrophobic	false
C24	CG2	VAL- 168	4.45	0	Hydrophobic	false
C29	CB	THR- 170	4.07	0	Hydrophobic	false
C16	CG1	VAL- 220	3.92	0	Hydrophobic	false
CL15	CE	MET- 221	3.83	0	Hydrophobic	false
C25	CG2	VAL- 223	3.83	0	Hydrophobic	false
N4	OE1	GLU- 224	3.24	126.65	H-Bond (Ligand Donor)	false
N4	OE2	GLU- 224	2.7	173.81	H-Bond (Ligand Donor)	false
N4	OE1	GLU- 224	3.24	0	Ionic (Ligand Cationic)	false
N4	OE2	GLU- 224	2.7	0	Ionic (Ligand Cationic)	false
CL15	CB	GLU- 224	3.78	0	Hydrophobic	false
O7	NE2	GLN- 231	3.28	137.3	H-Bond (Protein Donor)	false
C11	CB	GLN- 231	4.02	0	Hydrophobic	false
C8	CG	GLN- 231	3.63	0	Hydrophobic	false
CL15	CB	ALA- 234	3.93	0	Hydrophobic	false
C14	CB	ALA- 234	4.23	0	Hydrophobic	false
CL15	CD2	LEU- 235	3.25	0	Hydrophobic	false