scPDB - 1rbm entry

Protein Data Bank Entry:

PDB ID : 1rbm

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2003-11-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Trifunctional purine biosynthetic protein adenosine-3
ID:	PUR2_HUMAN
AC:	P22102
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.1.2.2

Chains:

Chain Name:	Percentage of Residues within binding site
A	92 %
B	8 %

Ligand binding site composition:

B-Factor:	25.167
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.339	1107.000

% Hydrophobic	% Polar
47.56	52.44
According to VolSite

Ligand :

HET Code:	KT5
Formula:	C42H48F3N9O20
Molecular weight:	1055.874 g/mol
DrugBank ID:	-
Buried Surface Area:	64.55 %
Polar Surface area:	524.79 Å2

Number of
H-Bond Acceptors:	24
H-Bond Donors:	10
Rings:	2
Aromatic rings:	2
Anionic atoms:	6
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	33

Mass center Coordinates

X	Y	Z
-6.04826	56.0331	15.7479

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
O11	CZ	ARG- 64	3.81	0	Ionic (Protein Cationic)	false
C3	CD1	LEU- 85	3.91	0	Hydrophobic	false
N1A	O	MET- 89	3.02	138.54	H-Bond (Ligand Donor)	false
C16	SD	MET- 89	4.06	0	Hydrophobic	false
F2	CE	MET- 89	3.31	0	Hydrophobic	false
O11	CZ	ARG- 90	3.84	0	Ionic (Protein Cationic)	false
O1A	CZ	ARG- 90	3.58	0	Ionic (Protein Cationic)	false
O1A	N	ILE- 91	2.9	170.92	H-Bond (Protein Donor)	false
C13	CD1	ILE- 91	3.94	0	Hydrophobic	false
C14	CG1	ILE- 91	3.88	0	Hydrophobic	false
N2	O	LEU- 92	2.87	172.59	H-Bond (Ligand Donor)	false
N1	N	LEU- 92	2.93	161.67	H-Bond (Protein Donor)	false
OA2	ND2	ASN- 106	3.06	149.82	H-Bond (Protein Donor)	false
C3	CB	ASN- 106	4.27	0	Hydrophobic	false
F3	CG	PRO- 109	4.17	0	Hydrophobic	false
F2	CB	SER- 118	3.56	0	Hydrophobic	false
C3	CG2	VAL- 139	4.43	0	Hydrophobic	false
N3	O	ALA- 140	2.76	127.84	H-Bond (Ligand Donor)	false
N2	O	GLU- 141	2.95	151.63	H-Bond (Ligand Donor)	false
C12	CG1	VAL- 143	3.37	0	Hydrophobic	false
C1	CG1	VAL- 143	3.69	0	Hydrophobic	false
OA2	OD2	ASP- 144	3.35	146.46	H-Bond (Ligand Donor)	false
OA1	OD2	ASP- 144	2.75	153.06	H-Bond (Ligand Donor)	false
O1	N	ASP- 144	3.07	155.15	H-Bond (Protein Donor)	false
CG1	CD2	LEU- 171	3.79	0	Hydrophobic	false
O1	O	HOH- 528	2.66	153.65	H-Bond (Protein Donor)	false
N2A	O	HOH- 580	2.55	175.4	H-Bond (Ligand Donor)	false