scPDB - 3d64 entry

Protein Data Bank Entry:

PDB ID : 3d64

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2008-05-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenosylhomocysteinase
ID:	SAHH_BURP1
AC:	Q3JY79
Organism:	Burkholderia pseudomallei
Reign:	Bacteria
TaxID:	320372
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	18 %
B	82 %

Ligand binding site composition:

B-Factor:	22.156
Number of residues:	54
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.170	2608.875

% Hydrophobic	% Polar
39.20	60.80
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	66.63 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
70.0099	2.9393	-4.2203

Binding mode :

What is Poseview ?

2D View
3D View

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
C4N	SG	CYS- 238	3.82	0	Hydrophobic	false
O2N	N	VAL- 267	2.96	162.22	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 267	4.12	0	Hydrophobic	false
C5N	CG2	VAL- 267	3.94	0	Hydrophobic	false
O3B	OE2	GLU- 286	2.74	157.99	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 286	2.72	154.62	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 286	3.45	143.24	H-Bond (Ligand Donor)	false
C2B	CG1	ILE- 287	4.31	0	Hydrophobic	false
C1B	CB	THR- 319	4.43	0	Hydrophobic	false
N7A	ND2	ASN- 321	2.94	155.37	H-Bond (Protein Donor)	false
N7N	O	ILE- 342	2.53	153.8	H-Bond (Ligand Donor)	false
O7N	ND2	ASN- 387	2.82	160.4	H-Bond (Protein Donor)	false
N7N	OD1	ASN- 387	3.18	163.6	H-Bond (Ligand Donor)	false
O3B	NZ	LYS- 467	2.73	136.45	H-Bond (Protein Donor)	false
O2A	OH	TYR- 471	2.58	158.75	H-Bond (Protein Donor)	false
O2N	O	HOH- 882	2.67	179.97	H-Bond (Protein Donor)	false