scPDB - 3dr4 entry

Protein Data Bank Entry:

PDB ID : 3dr4

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2008-07-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	GDP-perosamine synthase
ID:	GDPPS_CAUCR
AC:	Q9A9H3
Organism:	Caulobacter crescentus
Reign:	Bacteria
TaxID:	190650
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	24 %
B	76 %

Ligand binding site composition:

B-Factor:	26.480
Number of residues:	57
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.639	837.000

% Hydrophobic	% Polar
51.61	48.39
According to VolSite

Ligand :

HET Code:	G4M
Formula:	C24H33N7O19P3
Molecular weight:	816.476 g/mol
DrugBank ID:	-
Buried Surface Area:	69.99 %
Polar Surface area:	444.21 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	8
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
7.69428	-1.56598	43.5669

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
C4'	CG1	VAL- 9	4.04	0	Hydrophobic	false
C4'	CB	ALA- 10	4.29	0	Hydrophobic	false
N1	O	THR- 29	2.5	171.09	H-Bond (Ligand Donor)	false
N2	OG1	THR- 29	2.79	158.34	H-Bond (Ligand Donor)	false
C2'	CZ3	TRP- 30	4.45	0	Hydrophobic	false
O6	N	ILE- 31	3.04	154.4	H-Bond (Protein Donor)	false
N7	OG	SER- 32	2.9	165.05	H-Bond (Protein Donor)	false
O6	N	SER- 32	3.18	136.74	H-Bond (Protein Donor)	false
OP2	N	GLY- 60	2.82	150.26	H-Bond (Protein Donor)	false
OP1	N	THR- 61	2.91	141.16	H-Bond (Protein Donor)	false
OP1	OG1	THR- 61	2.66	159.86	H-Bond (Protein Donor)	false
C5B	CD2	TYR- 86	3.87	0	Hydrophobic	false
C2A	CB	TYR- 86	4.01	0	Hydrophobic	false
C5G	CE1	TYR- 86	3.97	0	Hydrophobic	false
C6G	CD1	TYR- 86	4.07	0	Hydrophobic	false
C3G	CZ	TYR- 86	4.02	0	Hydrophobic	false
C5B	CB	ALA- 88	3.97	0	Hydrophobic	false
C2A	CG1	VAL- 131	3.56	0	Hydrophobic	false
N1L	OD1	ASP- 157	3.18	120.63	H-Bond (Ligand Donor)	false
N1L	OD2	ASP- 157	2.81	172.52	H-Bond (Ligand Donor)	false
C2A	CB	ALA- 159	3.87	0	Hydrophobic	false
C2A	CG	GLU- 160	4.18	0	Hydrophobic	false
O3L	OE2	GLU- 160	2.64	141.11	H-Bond (Ligand Donor)	false
OP2	OG	SER- 181	2.77	166.74	H-Bond (Protein Donor)	false
C2G	CD2	PHE- 183	4.16	0	Hydrophobic	false
O5G	ND2	ASN- 185	3.29	148.88	H-Bond (Protein Donor)	false
C4'	CB	ASN- 185	4.02	0	Hydrophobic	false
O4P	CZ	ARG- 220	3.82	0	Ionic (Protein Cationic)	false
O4P	NH1	ARG- 220	2.79	141.99	H-Bond (Protein Donor)	false
C6G	CZ	TYR- 221	4.26	0	Hydrophobic	false
O3P	OH	TYR- 221	2.89	143.92	H-Bond (Protein Donor)	false
OP1	ND2	ASN- 229	2.83	165.26	H-Bond (Protein Donor)	false
C6G	CH2	TRP- 286	3.86	0	Hydrophobic	false
O3'	OE1	GLU- 313	2.55	134.15	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 313	3.36	164.17	H-Bond (Ligand Donor)	false
O3P	NE	ARG- 315	3.08	166.23	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 315	2.78	148.81	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 315	3.75	0	Ionic (Protein Cationic)	false
C6G	CE1	PHE- 318	3.82	0	Hydrophobic	false
OP2	O	HOH- 1294	2.86	163.04	H-Bond (Protein Donor)	false
OP3	O	HOH- 1295	2.64	179.97	H-Bond (Protein Donor)	false