scPDB - 5c1l entry

Protein Data Bank Entry:

PDB ID : 5c1l

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2015-06-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Histo-blood group ABO system transferase
ID:	BGAT_HUMAN
AC:	P16442
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.757
Number of residues:	33
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.532	702.000

% Hydrophobic	% Polar
44.23	55.77
According to VolSite

Ligand :

HET Code:	GDU
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB03501
Buried Surface Area:	57.92 %
Polar Surface area:	316.82 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
13.2281	20.1131	7.03028

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
C1D	CB	PHE- 121	4.35	0	Hydrophobic	false
O2D	O	PHE- 121	2.62	177.18	H-Bond (Ligand Donor)	false
N3	O	ILE- 123	2.88	168.65	H-Bond (Ligand Donor)	false
O2	N	ILE- 123	2.88	162.09	H-Bond (Protein Donor)	false
C3D	CE2	TYR- 126	3.77	0	Hydrophobic	false
C2D	CD2	TYR- 126	3.7	0	Hydrophobic	false
C3D	CB	ASP- 211	4.4	0	Hydrophobic	false
O3D	N	VAL- 212	3.08	144.46	H-Bond (Protein Donor)	false
C2D	CG1	VAL- 212	3.75	0	Hydrophobic	false
O3D	OD1	ASP- 213	2.8	137.98	H-Bond (Ligand Donor)	false
C6'	CZ3	TRP- 300	4.41	0	Hydrophobic	false
O4'	O	TRP- 300	2.82	140.56	H-Bond (Ligand Donor)	false
C4'	CB	HIS- 301	4.3	0	Hydrophobic	false
O4'	ND1	HIS- 301	3.07	156.98	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 302	2.67	150.9	H-Bond (Ligand Donor)	false
O3'	N	GLU- 303	3.12	131.08	H-Bond (Protein Donor)	false
C2'	CB	GLU- 303	4.03	0	Hydrophobic	false
O1A	MN	MN- 401	2.2	0	Metal Acceptor	false
O1B	MN	MN- 401	2.05	0	Metal Acceptor	false
O2D	O	HOH- 525	2.72	179.97	H-Bond (Protein Donor)	false
O2'	O	HOH- 560	2.73	161.62	H-Bond (Ligand Donor)	false