scPDB - 1ybm entry

Protein Data Bank Entry:

PDB ID : 1ybm

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2004-12-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein At5g02240
ID:	Y5224_ARATH
AC:	Q94EG6
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	32.770
Number of residues:	48
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.840	1039.500

% Hydrophobic	% Polar
43.83	56.17
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	62.8 %
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
59.8965	13.6547	6.33125

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
O1A	NH2	ARG- 15	3.41	159.12	H-Bond (Protein Donor)	false
O2A	NE	ARG- 15	3.1	159.67	H-Bond (Protein Donor)	false
O2A	N	ARG- 15	3.12	173.46	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 15	3.83	0	Ionic (Protein Cationic)	false
O1N	CZ	ARG- 15	3.39	0	Ionic (Protein Cationic)	false
O2N	N	THR- 16	2.67	151.83	H-Bond (Protein Donor)	false
O2N	OG1	THR- 16	2.61	161.75	H-Bond (Protein Donor)	false
C5D	CB	THR- 16	4.03	0	Hydrophobic	false
O1X	CZ	ARG- 38	3.68	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 38	3.53	0	Ionic (Protein Cationic)	false
O3X	NE	ARG- 38	3.04	139.95	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 38	3.22	132.82	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 56	3.09	171.9	H-Bond (Ligand Donor)	false
N1A	N	ILE- 57	3.09	171.78	H-Bond (Protein Donor)	false
C5D	CD2	LEU- 76	3.6	0	Hydrophobic	false
C1B	CG2	THR- 77	4.43	0	Hydrophobic	false
C5B	CB	SER- 78	3.91	0	Hydrophobic	false
C3D	CB	SER- 78	3.78	0	Hydrophobic	false
O4B	N	SER- 78	3.24	152.59	H-Bond (Protein Donor)	false
O2D	OG	SER- 78	3.39	171.6	H-Bond (Ligand Donor)	false
C5B	CG2	VAL- 80	4.34	0	Hydrophobic	false
N6A	OE1	GLN- 103	3.13	144.83	H-Bond (Ligand Donor)	false
C4D	CG1	VAL- 131	3.73	0	Hydrophobic	false
C5N	CB	SER- 133	3.87	0	Hydrophobic	false
O3D	NZ	LYS- 155	3	178.23	H-Bond (Protein Donor)	false
C5N	CB	ALA- 174	4.24	0	Hydrophobic	false
O7N	N	LEU- 177	2.71	168.39	H-Bond (Protein Donor)	false
C5D	CD1	LEU- 177	3.88	0	Hydrophobic	false
C3N	CG	LEU- 177	3.64	0	Hydrophobic	false
O1N	NH2	ARG- 205	2.96	156.13	H-Bond (Protein Donor)	false
O1N	NE	ARG- 205	3.43	137.82	H-Bond (Protein Donor)	false
O2N	NE	ARG- 205	3.12	155.19	H-Bond (Protein Donor)	false
O1N	CZ	ARG- 205	3.63	0	Ionic (Protein Cationic)	false