scPDB - 2apc entry

Protein Data Bank Entry:

PDB ID : 2apc

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2005-08-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
ID:	MGAT1_RABIT
AC:	P27115
Organism:	Oryctolagus cuniculus
Reign:	Eukaryota
TaxID:	9986
EC Number:	2.4.1.101

Chains:

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

Ligand binding site composition:

B-Factor:	13.012
Number of residues:	51
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	8
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.077	455.625

% Hydrophobic	% Polar
41.48	58.52
According to VolSite

Ligand :

HET Code:	UDM
Formula:	C18H27N3O16P2
Molecular weight:	603.365 g/mol
DrugBank ID:	-
Buried Surface Area:	64.65 %
Polar Surface area:	316.45 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
1.42862	19.1009	11.1656

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
O3D	O	ILE- 113	2.87	128.8	H-Bond (Ligand Donor)	false
C3D	CG2	ILE- 113	3.91	0	Hydrophobic	false
C2D	CB	CYS- 115	4.27	0	Hydrophobic	false
O1A	NH2	ARG- 117	2.84	148.82	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 117	3.41	127.85	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 117	3.54	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 117	3.83	0	Ionic (Protein Cationic)	false
N3	OD2	ASP- 144	2.86	166.91	H-Bond (Ligand Donor)	false
CB	CE2	TYR- 184	4.46	0	Hydrophobic	false
C5'	CD1	ILE- 187	4.13	0	Hydrophobic	false
C6'	CG2	ILE- 187	4.11	0	Hydrophobic	false
CB	CD1	ILE- 187	4.36	0	Hydrophobic	false
C1D	CG1	ILE- 187	4.17	0	Hydrophobic	false
C5D	CD1	ILE- 187	3.88	0	Hydrophobic	false
O2	ND1	HIS- 190	2.72	155.34	H-Bond (Protein Donor)	false
O3'	OE2	GLU- 211	2.63	166.1	H-Bond (Ligand Donor)	false
O4'	OE1	GLU- 211	2.67	164.97	H-Bond (Ligand Donor)	false
C4D	CG	GLU- 211	4.04	0	Hydrophobic	false
O3D	OD1	ASP- 212	3.08	133.51	H-Bond (Ligand Donor)	false
C8'	CD2	LEU- 269	3.84	0	Hydrophobic	false
C4'	CZ2	TRP- 290	4.11	0	Hydrophobic	false
C6'	CE2	TRP- 290	4.23	0	Hydrophobic	false
O4'	NE1	TRP- 290	2.91	134.04	H-Bond (Protein Donor)	false
O2A	N	VAL- 321	2.88	154.64	H-Bond (Protein Donor)	false
C8'	CD1	LEU- 331	3.56	0	Hydrophobic	false
O1A	MN	MN- 448	2.24	0	Metal Acceptor	false
O1B	MN	MN- 448	2.17	0	Metal Acceptor	false
O6'	O	HOH- 459	2.84	179.97	H-Bond (Protein Donor)	false
O7'	O	HOH- 646	2.89	179.95	H-Bond (Protein Donor)	false