scPDB - 4dqw entry

Protein Data Bank Entry:

PDB ID : 4dqw

Resolution :2.510 Å

Experimental Method : X-ray

Deposition Date : 2012-02-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Inosine-5'-monophosphate dehydrogenase
ID:	Q9HXM5_PSEAE
AC:	Q9HXM5
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	79 %
B	21 %

Ligand binding site composition:

B-Factor:	43.972
Number of residues:	34
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	7
Water Molecules:	0
Cofactors:	ATP ATP ATP
Metals:	MN MN MN MN

Cavity properties

Ligandability	Volume (Å3)
0.054	583.875

% Hydrophobic	% Polar
45.66	54.34
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	74.03 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-5.86552	-24.1439	32.0862

Binding mode :

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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
O2B	OG1	THR- 134	2.61	169.51	H-Bond (Protein Donor)	false
C2'	CG2	THR- 134	3.95	0	Hydrophobic	false
O2B	N	ARG- 136	3.33	151.43	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 136	3.16	122.1	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 136	3.09	149.31	H-Bond (Protein Donor)	false
O3A	NH2	ARG- 136	3.19	157.3	H-Bond (Protein Donor)	false
C5'	CD	ARG- 136	3.83	0	Hydrophobic	false
C3'	CB	ARG- 136	4.25	0	Hydrophobic	false
O3'	OD1	ASP- 137	3.48	145.28	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 137	2.76	156.03	H-Bond (Ligand Donor)	false
O2'	OG1	THR- 153	3.04	170.72	H-Bond (Protein Donor)	false
N6	O	VAL- 159	3.19	167.9	H-Bond (Ligand Donor)	false
N1	N	VAL- 159	2.84	166.34	H-Bond (Protein Donor)	false
C3'	CG	ARG- 178	4.09	0	Hydrophobic	false
O2A	N	GLU- 180	2.83	132.21	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 181	3.33	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 181	2.82	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 181	2.82	160.37	H-Bond (Protein Donor)	false
N6	O	LYS- 181	3.1	139.21	H-Bond (Ligand Donor)	false
O1G	MN	MN- 502	2.28	0	Metal Acceptor	false
O3G	MN	MN- 502	1.91	0	Metal Acceptor	false
O1B	MN	MN- 502	2.17	0	Metal Acceptor	false
O1G	MN	MN- 504	2.14	0	Metal Acceptor	false