scPDB - 3ahi entry

Protein Data Bank Entry:

PDB ID : 3ahi

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2010-04-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Probable phosphoketolase
ID:	D6PAH1_BIFBR
AC:	D6PAH1
Organism:	Bifidobacterium breve
Reign:	Bacteria
TaxID:	1685
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.496
Number of residues:	36
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.968	330.750

% Hydrophobic	% Polar
67.35	32.65
According to VolSite

Ligand :

HET Code:	HTL
Formula:	C14H18N4O8P2S
Molecular weight:	464.327 g/mol
DrugBank ID:	DB02410
Buried Surface Area:	56.59 %
Polar Surface area:	242.39 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
63.3361	48.7883	10.9574

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
O22	OG1	THR- 67	2.65	154.9	H-Bond (Protein Donor)	false
O23	NE2	HIS- 97	2.76	171.88	H-Bond (Protein Donor)	false
C3'	CB	HIS- 97	3.82	0	Hydrophobic	false
N4'	O	GLY- 155	2.75	140.84	H-Bond (Ligand Donor)	false
C2A	CG	GLU- 156	3.86	0	Hydrophobic	false
C2A	CB	LEU- 157	4.31	0	Hydrophobic	false
S1	CD1	LEU- 157	4.09	0	Hydrophobic	false
C5B	CD1	LEU- 157	3.65	0	Hydrophobic	false
N3'	N	LEU- 157	3.1	166.62	H-Bond (Protein Donor)	false
O12	N	GLY- 183	2.72	152.27	H-Bond (Protein Donor)	false
O13	N	GLU- 184	2.92	149.98	H-Bond (Protein Donor)	false
O21	ND2	ASN- 215	2.99	144.31	H-Bond (Protein Donor)	false
O22	ND2	ASN- 215	3.19	138.59	H-Bond (Protein Donor)	false
C5A	CB	LYS- 218	3.83	0	Hydrophobic	false
S1	CG1	ILE- 219	4.23	0	Hydrophobic	false
C4A	CD1	ILE- 219	3.79	0	Hydrophobic	false
C5A	CG1	ILE- 219	3.66	0	Hydrophobic	false
O21	NZ	LYS- 300	2.65	162.29	H-Bond (Protein Donor)	false
O21	NZ	LYS- 300	2.65	0	Ionic (Protein Cationic)	false
O23	NZ	LYS- 300	3.24	0	Ionic (Protein Cationic)	false
O12	MG	MG- 826	2	0	Metal Acceptor	false
O21	MG	MG- 826	2.11	0	Metal Acceptor	false
O23	O	HOH- 888	3.08	125.27	H-Bond (Protein Donor)	false
O22	O	HOH- 1222	2.64	121.09	H-Bond (Protein Donor)	false