scPDB - 1n1d entry

Protein Data Bank Entry:

PDB ID : 1n1d

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2002-10-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycerol-3-phosphate cytidylyltransferase
ID:	TAGD_BACSU
AC:	P27623
Organism:	Bacillus subtilis
Reign:	Bacteria
TaxID:	224308
EC Number:	2.7.7.39

Chains:

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

Ligand binding site composition:

B-Factor:	8.979
Number of residues:	39
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.017	668.250

% Hydrophobic	% Polar
39.90	60.10
According to VolSite

Ligand :

HET Code:	C2G
Formula:	C12H19N3O13P2
Molecular weight:	475.239 g/mol
DrugBank ID:	DB02484
Buried Surface Area:	76.99 %
Polar Surface area:	276.4 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	5
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
38.0969	56.283	49.0001

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
C1G	CB	TYR- 7	4.08	0	Hydrophobic	false
O1A	N	THR- 9	3.41	127.76	H-Bond (Protein Donor)	false
O3A	N	THR- 9	3	165.94	H-Bond (Protein Donor)	false
C4'	CE2	PHE- 10	4.14	0	Hydrophobic	false
C5'	CZ	PHE- 10	4.05	0	Hydrophobic	false
O1A	N	PHE- 10	2.85	154.16	H-Bond (Protein Donor)	false
C1'	CG	LEU- 20	3.78	0	Hydrophobic	false
C4'	CG	LEU- 20	4.15	0	Hydrophobic	false
C2G	CE2	PHE- 40	4.5	0	Hydrophobic	false
O1B	NZ	LYS- 44	3.19	169.69	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 44	3.34	165.13	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 44	3.19	0	Ionic (Protein Cationic)	false
C3G	CD	LYS- 44	3.51	0	Hydrophobic	false
O2A	NZ	LYS- 46	3.79	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 46	2.82	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 46	2.82	160.46	H-Bond (Protein Donor)	false
O1G	OE1	GLU- 71	3.03	159.17	H-Bond (Ligand Donor)	false
O2G	OE1	GLU- 71	2.69	170.89	H-Bond (Ligand Donor)	false
C2G	CZ3	TRP- 74	4.36	0	Hydrophobic	false
O1G	NZ	LYS- 77	3.07	170.7	H-Bond (Protein Donor)	false
C3'	CE	MET- 91	4.21	0	Hydrophobic	false
C1G	CE	MET- 91	3.71	0	Hydrophobic	false
C3G	CE	MET- 91	4.48	0	Hydrophobic	false
O3'	N	GLY- 92	2.98	151.09	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 94	2.83	154.21	H-Bond (Ligand Donor)	false
O2B	NE1	TRP- 95	3.1	155.71	H-Bond (Protein Donor)	false
C3G	CZ2	TRP- 95	3.58	0	Hydrophobic	false
C1G	CZ	PHE- 99	3.86	0	Hydrophobic	false
N3	N	THR- 114	3.06	168.89	H-Bond (Protein Donor)	false
N4	O	THR- 114	2.68	141.94	H-Bond (Ligand Donor)	false
N4	O	ILE- 117	2.99	159.76	H-Bond (Ligand Donor)	false