scPDB - 2dr3 entry

Protein Data Bank Entry:

PDB ID : 2dr3

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2006-06-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UPF0273 protein PH0284
ID:	Y284_PYRHO
AC:	O58022
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
D	62 %
E	38 %

Ligand binding site composition:

B-Factor:	41.242
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.837	1731.375

% Hydrophobic	% Polar
42.88	57.12
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	65.42 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
49.9841	-38.6941	127.096

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
O2B	N	GLY- 33	2.85	158.89	H-Bond (Protein Donor)	false
O1B	N	THR- 34	3.3	135.02	H-Bond (Protein Donor)	false
O1B	N	GLY- 35	3.1	125.35	H-Bond (Protein Donor)	false
O3A	N	GLY- 35	3.35	150.11	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 36	2.77	157.81	H-Bond (Protein Donor)	false
O1B	N	LYS- 36	2.98	155.56	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 36	2.77	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 36	3.77	0	Ionic (Protein Cationic)	false
O3B	N	THR- 37	3.38	156.88	H-Bond (Protein Donor)	false
O1A	N	THR- 37	3.22	120.79	H-Bond (Protein Donor)	false
O1A	N	ILE- 38	3.29	176.57	H-Bond (Protein Donor)	false
C5'	CD1	ILE- 38	4.2	0	Hydrophobic	false
O3'	N	MET- 212	3.14	158.59	H-Bond (Protein Donor)	false
O2'	NE2	HIS- 217	2.73	150.3	H-Bond (Ligand Donor)	false
C4'	CD1	ILE- 226	4.1	0	Hydrophobic	false
C1'	CG2	ILE- 226	4.06	0	Hydrophobic	false
O3'	O	HOH- 3846	2.69	148.65	H-Bond (Ligand Donor)	false