scPDB - 5d4v entry

Protein Data Bank Entry:

PDB ID : 5d4v

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2015-08-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein MJ0489
ID:	Y489_METJA
AC:	Q57913
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	48 %
D	52 %

Ligand binding site composition:

B-Factor:	31.639
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.151	1292.625

% Hydrophobic	% Polar
48.04	51.96
According to VolSite

Ligand :

HET Code:	YGP
Formula:	C17H20N6O9P
Molecular weight:	483.349 g/mol
DrugBank ID:	-
Buried Surface Area:	36.84 %
Polar Surface area:	232.48 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	4
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
24.5782	-1.24645	-17.2276

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
C1'	CD1	TYR- 156	4	0	Hydrophobic	false
C1'	CD1	TYR- 156	4.43	0	Hydrophobic	false
C2'	CG	TYR- 156	3.42	0	Hydrophobic	false
C3'	CD1	TYR- 156	3.78	0	Hydrophobic	false
OAI	NZ	LYS- 157	3.8	0	Ionic (Protein Cationic)	false
OAF	NZ	LYS- 157	2.96	0	Ionic (Protein Cationic)	false
OAF	NZ	LYS- 157	2.96	138.4	H-Bond (Protein Donor)	false
CAB	CB	ALA- 160	4.03	0	Hydrophobic	false
CAB	CG1	ILE- 163	4.35	0	Hydrophobic	false
N2	OE2	GLU- 266	3.14	156.32	H-Bond (Ligand Donor)	false