scPDB - 1d7a entry

Protein Data Bank Entry:

PDB ID : 1d7a

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1999-10-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N5-carboxyaminoimidazole ribonucleotide mutase
ID:	PURE_ECOLI
AC:	P0AG18
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	84 %
N	16 %

Ligand binding site composition:

B-Factor:	21.635
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.759	540.000

% Hydrophobic	% Polar
41.88	58.13
According to VolSite

Ligand :

HET Code:	AIR
Formula:	C8H12N3O7P
Molecular weight:	293.171 g/mol
DrugBank ID:	-
Buried Surface Area:	58.51 %
Polar Surface area:	175.76 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	2
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
30.6192	10.9162	19.09

Binding mode :

What is Poseview ?

2D View
3D View

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
O6	OG	SER- 16	2.98	141.44	H-Bond (Protein Donor)	false
C3'	CB	SER- 16	4.14	0	Hydrophobic	false
O6	OG	SER- 18	3.07	140.23	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 19	3	140.49	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 19	2.55	162.03	H-Bond (Ligand Donor)	false
O8	NH1	ARG- 46	3.21	130.37	H-Bond (Protein Donor)	false
O8	NH2	ARG- 46	2.71	153.68	H-Bond (Protein Donor)	false
O8	CZ	ARG- 46	3.37	0	Ionic (Protein Cationic)	false
C2'	CB	ALA- 70	4.48	0	Hydrophobic	false
O2'	N	GLY- 71	3.4	148.97	H-Bond (Protein Donor)	false
O3'	N	GLY- 71	2.82	122.2	H-Bond (Protein Donor)	false
C1'	CB	PRO- 111	4.43	0	Hydrophobic	false