scPDB - 2azn entry

Protein Data Bank Entry:

PDB ID : 2azn

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2005-09-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase
ID:	RIB7_METJA
AC:	Q58085
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	48.685
Number of residues:	45
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.288	418.500

% Hydrophobic	% Polar
36.29	63.71
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	63.92 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-6.97906	-51.2956	-45.2084

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
C3N	CG2	VAL- 15	4.09	0	Hydrophobic	false
O7N	N	GLY- 16	3.15	149.49	H-Bond (Protein Donor)	false
N7N	O	GLY- 16	2.84	125.86	H-Bond (Ligand Donor)	false
C3N	CD1	LEU- 23	3.94	0	Hydrophobic	false
O3D	OD1	ASN- 28	3.49	143.75	H-Bond (Ligand Donor)	false
C4B	CG2	ILE- 55	3.62	0	Hydrophobic	false
C1B	CG2	ILE- 55	3.88	0	Hydrophobic	false
O1A	OG1	THR- 57	3.24	153.06	H-Bond (Protein Donor)	false
O1A	N	THR- 57	3.49	141.43	H-Bond (Protein Donor)	false
C3D	CB	THR- 57	4.45	0	Hydrophobic	false
C2D	CG2	THR- 57	4.25	0	Hydrophobic	false
C5N	CG2	THR- 57	3.96	0	Hydrophobic	false
O2N	NZ	LYS- 60	3.96	0	Ionic (Protein Cationic)	false
C3D	CD	LYS- 60	4.03	0	Hydrophobic	false
O2D	OD1	ASP- 61	2.97	164.35	H-Bond (Ligand Donor)	false
O2X	N	SER- 83	2.78	138.03	H-Bond (Protein Donor)	false
O3X	OG	SER- 83	3.08	138.27	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 84	3.36	153.73	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 84	3.36	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 84	3.57	0	Ionic (Protein Cationic)	false
O1X	CZ	ARG- 86	3.93	0	Ionic (Protein Cationic)	false
N7A	N	VAL- 134	3.22	146.4	H-Bond (Protein Donor)	false
N6A	O	VAL- 134	2.95	143.55	H-Bond (Ligand Donor)	false
O1A	N	GLY- 156	2.8	140.88	H-Bond (Protein Donor)	false
C3B	CG2	THR- 158	3.69	0	Hydrophobic	false
O1N	N	THR- 158	2.83	151.08	H-Bond (Protein Donor)	false
O1N	OG1	THR- 158	2.65	154.46	H-Bond (Protein Donor)	false
O2A	N	LEU- 159	2.75	157.22	H-Bond (Protein Donor)	false
C5D	CB	PRO- 187	3.9	0	Hydrophobic	false