scPDB - 2dv5 entry

Protein Data Bank Entry:

PDB ID : 2dv5

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2006-07-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Diphthine synthase
ID:	DPHB_PYRHO
AC:	O58456
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
B	3 %

Ligand binding site composition:

B-Factor:	35.106
Number of residues:	41
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.077	479.250

% Hydrophobic	% Polar
47.18	52.82
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	76.62 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
28.1723	90.3641	66.2413

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
N6	O	LEU- 10	3.38	143.35	H-Bond (Ligand Donor)	false
C5'	CB	SER- 37	3.67	0	Hydrophobic	false
CG	CB	SER- 37	4.15	0	Hydrophobic	false
N	O	ASP- 87	2.83	131.12	H-Bond (Ligand Donor)	false
O	N	ASP- 87	2.89	171.88	H-Bond (Protein Donor)	false
N	O	VAL- 90	2.64	161.49	H-Bond (Ligand Donor)	false
SD	CB	ALA- 91	3.84	0	Hydrophobic	false
CG	CB	ALA- 91	3.85	0	Hydrophobic	false
CG	CG2	THR- 92	4.41	0	Hydrophobic	false
O	OG	SER- 115	2.72	150.05	H-Bond (Protein Donor)	false
CB	CG2	ILE- 116	4.36	0	Hydrophobic	false
C1'	CG1	ILE- 116	4.19	0	Hydrophobic	false
OXT	N	ILE- 116	3.09	172.32	H-Bond (Protein Donor)	false
SD	CD1	PHE- 165	3.89	0	Hydrophobic	false
C4'	CD1	PHE- 165	4.02	0	Hydrophobic	false
C1'	CD1	PHE- 165	4.33	0	Hydrophobic	false
O3'	O	LEU- 166	2.69	142.03	H-Bond (Ligand Donor)	false
O2'	N	LEU- 166	3.04	162.88	H-Bond (Protein Donor)	false
N6	O	ALA- 209	2.72	136.02	H-Bond (Ligand Donor)	false
N1	N	ALA- 209	3	150.74	H-Bond (Protein Donor)	false
C2'	CB	PRO- 233	4.05	0	Hydrophobic	false
O2'	O	HIS- 234	2.76	147.09	H-Bond (Ligand Donor)	false
C1'	CD1	ILE- 235	3.49	0	Hydrophobic	false
N	O	HOH- 1696	2.79	140.74	H-Bond (Ligand Donor)	false