scPDB - 1qf5 entry

Protein Data Bank Entry:

PDB ID : 1qf5

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1999-04-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenylosuccinate synthetase
ID:	PURA_ECOLI
AC:	P0A7D4
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	38.154
Number of residues:	46
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:	GDP
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.556	540.000

% Hydrophobic	% Polar
40.63	59.38
According to VolSite

Ligand :

HET Code:	RPL
Formula:	C13H18N3O13P
Molecular weight:	455.268 g/mol
DrugBank ID:	DB04460
Buried Surface Area:	78.35 %
Polar Surface area:	267.99 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
28.5551	17.1443	23.0846

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
OAA	OD1	ASP- 13	3.42	139.23	H-Bond (Ligand Donor)	false
O2P	ND2	ASN- 38	2.79	153.48	H-Bond (Protein Donor)	false
C5'	CG2	ILE- 126	4.14	0	Hydrophobic	false
C5'	CG2	THR- 128	4.15	0	Hydrophobic	false
O3P	OG1	THR- 129	2.97	170.26	H-Bond (Protein Donor)	false
O3P	N	THR- 129	2.88	171.25	H-Bond (Protein Donor)	false
C2'	CG2	THR- 129	4.02	0	Hydrophobic	false
C8A	CG2	THR- 129	4.36	0	Hydrophobic	false
O2P	OG1	THR- 239	2.91	160.84	H-Bond (Protein Donor)	false
C5'	CB	THR- 239	4.37	0	Hydrophobic	false
O3'	O	VAL- 273	3.22	150.45	H-Bond (Ligand Donor)	false
C7A	CG1	VAL- 273	3.29	0	Hydrophobic	false
CBA	CB	ALA- 299	4.31	0	Hydrophobic	false
OBA	N	ALA- 299	3.33	126.62	H-Bond (Protein Donor)	false
C8A	CB	THR- 300	4.04	0	Hydrophobic	false
CBA	CB	THR- 300	4.29	0	Hydrophobic	false
OJA	N	THR- 300	3.28	140.35	H-Bond (Protein Donor)	false
OJA	N	THR- 301	2.73	152.98	H-Bond (Protein Donor)	false
OJA	OG1	THR- 301	2.73	174.35	H-Bond (Protein Donor)	false
O2'	NH2	ARG- 303	2.66	143.3	H-Bond (Protein Donor)	false
OKA	NH2	ARG- 303	2.52	168.22	H-Bond (Protein Donor)	false
OKA	NE	ARG- 303	3.33	126.89	H-Bond (Protein Donor)	false
OKA	CZ	ARG- 303	3.34	0	Ionic (Protein Cationic)	false
OAA	NH1	ARG- 305	3.21	145.58	H-Bond (Protein Donor)	false
OBA	MG	MG- 433	2.26	0	Metal Acceptor	false
O4	O	HOH- 440	2.57	179.98	H-Bond (Protein Donor)	false
O3P	O	HOH- 443	2.63	179.94	H-Bond (Protein Donor)	false