scPDB - 5c1d entry

Protein Data Bank Entry:

PDB ID : 5c1d

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2015-06-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
ID:	OGT1_HUMAN
AC:	O15294
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %
C	0 %

Ligand binding site composition:

B-Factor:	32.819
Number of residues:	47
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.492	405.000

% Hydrophobic	% Polar
35.83	64.17
According to VolSite

Ligand :

HET Code:	12V
Formula:	C17H25N3O16P2S
Molecular weight:	621.403 g/mol
DrugBank ID:	-
Buried Surface Area:	70.93 %
Polar Surface area:	341.76 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:	10

Mass center Coordinates

X	Y	Z
12.4707	-45.8646	-29.3344

Binding mode :

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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
O7'	NE2	HIS- 498	3.04	158.42	H-Bond (Protein Donor)	false
C3B	CG	PRO- 559	4.35	0	Hydrophobic	false
S5'	CB	PRO- 559	3.37	0	Hydrophobic	false
C5'	CD1	LEU- 563	4.17	0	Hydrophobic	false
O4'	O	LEU- 653	2.58	166.99	H-Bond (Ligand Donor)	false
C8'	CG	PRO- 656	4.1	0	Hydrophobic	false
C4'	CZ	PHE- 694	4.42	0	Hydrophobic	false
O2A	NE2	GLN- 839	2.76	160.57	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 842	3.28	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 842	2.69	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 842	2.69	171.79	H-Bond (Protein Donor)	false
N3	O	ALA- 896	2.76	162.67	H-Bond (Ligand Donor)	false
O4	N	ALA- 896	2.83	175.11	H-Bond (Protein Donor)	false
C1B	CD	LYS- 898	4.46	0	Hydrophobic	false
O2'	NZ	LYS- 898	2.75	159.58	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 898	3	121.76	H-Bond (Protein Donor)	false
C8'	SG	CYS- 917	3.81	0	Hydrophobic	false
C1'	CB	HIS- 920	4.41	0	Hydrophobic	false
C3'	CB	HIS- 920	3.54	0	Hydrophobic	false
O1B	N	HIS- 920	2.9	154.5	H-Bond (Protein Donor)	false
O3'	ND1	HIS- 920	2.63	158.09	H-Bond (Ligand Donor)	false
O1'	OG1	THR- 921	2.77	155.85	H-Bond (Protein Donor)	false
O1'	N	THR- 921	2.97	145.75	H-Bond (Protein Donor)	false
C1'	CB	THR- 921	4.36	0	Hydrophobic	false
C3B	CG2	THR- 921	3.84	0	Hydrophobic	false
O1B	N	THR- 922	2.94	170.14	H-Bond (Protein Donor)	false
O1B	OG1	THR- 922	2.73	160.89	H-Bond (Protein Donor)	false
O3A	OG1	THR- 922	3.45	129.94	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 925	2.61	168.57	H-Bond (Ligand Donor)	false