scPDB - 3h86 entry

Protein Data Bank Entry:

PDB ID : 3h86

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2009-04-28

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:	KADA_METMP
AC:	Q6LYG0
Organism:	Methanococcus maripaludis
Reign:	Archaea
TaxID:	267377
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
G	100 %

Ligand binding site composition:

B-Factor:	50.398
Number of residues:	50
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.000	1147.500

% Hydrophobic	% Polar
43.24	56.76
According to VolSite

Ligand :

HET Code:	AP5
Formula:	C20H24N10O22P5
Molecular weight:	911.327 g/mol
DrugBank ID:	DB01717
Buried Surface Area:	60.73 %
Polar Surface area:	543.69 Å2

Number of
H-Bond Acceptors:	30
H-Bond Donors:	6
Rings:	6
Aromatic rings:	4
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
13.5842	-17.6537	-37.6093

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
O3G	N	GLY- 13	3.05	148.85	H-Bond (Protein Donor)	false
O2D	N	GLY- 13	3.15	132.24	H-Bond (Protein Donor)	false
O2D	N	VAL- 14	3.01	122.19	H-Bond (Protein Donor)	false
O2D	N	GLY- 15	2.56	145.68	H-Bond (Protein Donor)	false
O1D	OG1	THR- 17	3.49	150.09	H-Bond (Protein Donor)	false
O1D	N	THR- 17	2.85	167.54	H-Bond (Protein Donor)	false
O2E	OG1	THR- 18	2.83	137.3	H-Bond (Protein Donor)	false
O2E	N	THR- 18	2.88	142.21	H-Bond (Protein Donor)	false
C4J	CG2	THR- 18	4.5	0	Hydrophobic	false
O2J	OG1	THR- 18	3	165.98	H-Bond (Ligand Donor)	false
C1F	SD	MET- 43	4.44	0	Hydrophobic	false
O1A	NH2	ARG- 56	3.23	120.75	H-Bond (Protein Donor)	false
O5F	NH2	ARG- 56	3.34	170.89	H-Bond (Protein Donor)	false
C3F	CB	ARG- 60	4.36	0	Hydrophobic	false
N1A	NE2	GLN- 71	2.91	126.07	H-Bond (Protein Donor)	false
N7A	OG1	THR- 91	3.08	135.09	H-Bond (Protein Donor)	false
N6A	OG1	THR- 91	2.77	170.74	H-Bond (Ligand Donor)	false
O3A	NE2	HIS- 92	2.86	156.68	H-Bond (Protein Donor)	false
C2F	CG1	VAL- 95	4.09	0	Hydrophobic	false
N6A	O	GLY- 104	2.91	175.18	H-Bond (Ligand Donor)	false
C2J	CD	ARG- 131	3.58	0	Hydrophobic	false
C5J	CB	ASP- 135	4.01	0	Hydrophobic	false
O2B	CZ	ARG- 138	3.01	0	Ionic (Protein Cationic)	false
O2J	ND2	ASN- 175	3.06	128.62	H-Bond (Protein Donor)	false
N3B	ND2	ASN- 175	3.21	132.84	H-Bond (Protein Donor)	false