scPDB - 5c3a entry

Protein Data Bank Entry:

PDB ID : 5c3a

Resolution :1.330 Å

Experimental Method : X-ray

Deposition Date : 2015-06-17

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:	22.132
Number of residues:	36
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.642	712.125

% Hydrophobic	% Polar
43.13	56.87
According to VolSite

Ligand :

HET Code:	URM
Formula:	C16H24N2O16P2
Molecular weight:	562.313 g/mol
DrugBank ID:	-
Buried Surface Area:	56.93 %
Polar Surface area:	307.59 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:	9

Mass center Coordinates

X	Y	Z
12.9411	18.726	-6.76789

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
C1	CB	PHE- 121	4.43	0	Hydrophobic	false
O21	O	PHE- 121	2.61	175.22	H-Bond (Ligand Donor)	false
N15	O	ILE- 123	2.86	170.05	H-Bond (Ligand Donor)	false
O19	N	ILE- 123	2.86	159.88	H-Bond (Protein Donor)	false
C3	CE2	TYR- 126	3.72	0	Hydrophobic	false
C2	CD2	TYR- 126	3.68	0	Hydrophobic	false
O11	OH	TYR- 126	2.61	120.5	H-Bond (Protein Donor)	false
C1	CG1	VAL- 184	4.28	0	Hydrophobic	false
C5	CB	SER- 185	4.32	0	Hydrophobic	false
O7	N	VAL- 212	3.14	146.65	H-Bond (Protein Donor)	false
C2	CG1	VAL- 212	3.72	0	Hydrophobic	false
O7	OD1	ASP- 213	2.91	130.16	H-Bond (Ligand Donor)	false
O42	NE2	HIS- 233	3.2	144.85	H-Bond (Protein Donor)	false
O43	NE2	HIS- 233	2.9	138.4	H-Bond (Protein Donor)	false
C40	SD	MET- 266	4.06	0	Hydrophobic	false
C39	CE3	TRP- 300	3.9	0	Hydrophobic	false
C46	CH2	TRP- 300	4.14	0	Hydrophobic	false
C38	CZ3	TRP- 300	3.83	0	Hydrophobic	false
O43	OE1	GLU- 303	2.61	168.45	H-Bond (Ligand Donor)	false
O43	OE2	GLU- 303	3.33	123.37	H-Bond (Ligand Donor)	false
O44	OE2	GLU- 303	2.61	157.24	H-Bond (Ligand Donor)	false
O23	NZ	LYS- 346	3.66	0	Ionic (Protein Cationic)	false
O24	NZ	LYS- 346	3.3	0	Ionic (Protein Cationic)	false
O24	NZ	LYS- 346	3.3	164.08	H-Bond (Protein Donor)	false
O10	MN	MN- 401	2.21	0	Metal Acceptor	false
O24	MN	MN- 401	2.16	0	Metal Acceptor	false
O21	O	HOH- 534	2.7	149.94	H-Bond (Protein Donor)	false