scPDB - 4x9d entry

Protein Data Bank Entry:

PDB ID : 4x9d

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2014-12-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein MJ1435
ID:	Y1435_METJA
AC:	Q58830
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	28 %
C	56 %
D	17 %

Ligand binding site composition:

B-Factor:	16.992
Number of residues:	24
Including
Standard Amino Acids:	18
Non Standard Amino Acids:	5
Water Molecules:	1
Cofactors:
Metals:	NA NA NA

Cavity properties

Ligandability	Volume (Å3)
0.759	469.125

% Hydrophobic	% Polar
55.40	44.60
According to VolSite

Ligand :

HET Code:	U5P
Formula:	C9H11N2O9P
Molecular weight:	322.165 g/mol
DrugBank ID:	-
Buried Surface Area:	49.85 %
Polar Surface area:	181.33 Å2

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

Mass center Coordinates

X	Y	Z
112.226	-1.28171	25.3985

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
N3	OE2	GLU- 18	3.2	138.62	H-Bond (Ligand Donor)	false
C5'	CD1	TYR- 48	4.1	0	Hydrophobic	false
C2'	CD1	TYR- 48	3.55	0	Hydrophobic	false
C2'	CD1	PHE- 62	4.49	0	Hydrophobic	false
O2	NZ	LYS- 63	3.28	172.78	H-Bond (Protein Donor)	false
C1'	CD	LYS- 63	3.91	0	Hydrophobic	false
O3'	ND1	HIS- 64	2.75	151.61	H-Bond (Ligand Donor)	false
C5'	CB	HIS- 64	4.25	0	Hydrophobic	false