scPDB - 1dvr entry

Protein Data Bank Entry:

PDB ID : 1dvr

Resolution :2.360 Å

Experimental Method : X-ray

Deposition Date : 1995-12-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenylate kinase
ID:	KAD2_YEAST
AC:	P07170
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	92 %
B	8 %

Ligand binding site composition:

B-Factor:	19.532
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.775	955.125

% Hydrophobic	% Polar
42.76	57.24
According to VolSite

Ligand :

HET Code:	ATF
Formula:	C11H12F2N5O12P3
Molecular weight:	537.157 g/mol
DrugBank ID:	-
Buried Surface Area:	72.85 %
Polar Surface area:	310.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
22.3673	43.5426	-21.3785

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- 16	2.78	161.18	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 17	3.12	168.05	H-Bond (Protein Donor)	false
O2B	N	LYS- 17	3.01	145.57	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 17	3.49	133.76	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 17	3.12	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 17	3.49	0	Ionic (Protein Cationic)	false
F2B	CB	LYS- 17	3.57	0	Hydrophobic	false
O3A	N	GLY- 18	3.47	150.82	H-Bond (Protein Donor)	false
O2A	OG1	THR- 19	2.84	169.68	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 55	3.55	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 55	2.75	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 55	2.75	174.56	H-Bond (Protein Donor)	false
O3G	NE2	GLN- 59	3.27	142.88	H-Bond (Protein Donor)	false
C4'	CB	ARG- 128	4.46	0	Hydrophobic	false
C1'	CD	ARG- 128	4.3	0	Hydrophobic	false
DuAr	CZ	ARG- 128	3.7	9.31	Pi/Cation	false
O2G	NH1	ARG- 132	3.24	149.42	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 132	3.04	162.34	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 132	3.92	0	Ionic (Protein Cationic)	false
O1B	CZ	ARG- 132	4	0	Ionic (Protein Cationic)	false
C3'	CD	ARG- 132	3.66	0	Hydrophobic	false
O1A	OG	SER- 141	2.78	165.46	H-Bond (Protein Donor)	false
O2A	OG	SER- 141	3	123.47	H-Bond (Protein Donor)	false
C3'	CB	SER- 141	4.18	0	Hydrophobic	false
O2'	O	TYR- 142	3.45	163.23	H-Bond (Ligand Donor)	false
C2'	CB	HIS- 143	4.39	0	Hydrophobic	false
N6	O	GLN- 204	2.79	176.05	H-Bond (Ligand Donor)	false