scPDB - 4rkf entry

Protein Data Bank Entry:

PDB ID : 4rkf

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2014-10-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ras-related protein Rab-3
ID:	RAB3_DROME
AC:	P25228
Organism:	Drosophila melanogaster
Reign:	Eukaryota
TaxID:	7227
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	10.744
Number of residues:	41
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.334	361.125

% Hydrophobic	% Polar
54.21	45.79
According to VolSite

Ligand :

HET Code:	GNP
Formula:	C10H13N6O13P3
Molecular weight:	518.164 g/mol
DrugBank ID:	DB02082
Buried Surface Area:	82.11 %
Polar Surface area:	338.36 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
24.7918	3.53122	143.621

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
O1G	OG	SER- 30	2.66	172.61	H-Bond (Protein Donor)	false
C5'	CB	SER- 31	4.46	0	Hydrophobic	false
O1B	N	GLY- 33	2.94	155.04	H-Bond (Protein Donor)	false
O3A	N	GLY- 33	3.31	122.22	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 34	2.69	154.83	H-Bond (Protein Donor)	false
O1B	N	LYS- 34	2.92	164.23	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 34	2.86	156.39	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 34	2.69	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 34	2.86	0	Ionic (Protein Cationic)	false
O2B	N	THR- 35	2.98	167.87	H-Bond (Protein Donor)	false
O1A	OG	SER- 36	2.81	160.78	H-Bond (Protein Donor)	false
O1A	N	SER- 36	2.82	151.56	H-Bond (Protein Donor)	false
C2'	CZ	PHE- 46	4.26	0	Hydrophobic	false
O2'	O	THR- 47	2.72	153.65	H-Bond (Ligand Donor)	false
C5'	CD1	PHE- 50	3.54	0	Hydrophobic	false
C3'	CB	PHE- 50	3.81	0	Hydrophobic	false
O1G	OG	SER- 52	2.73	165.3	H-Bond (Protein Donor)	false
O2G	N	THR- 53	2.85	167.38	H-Bond (Protein Donor)	false
O3G	N	GLY- 79	2.81	145.47	H-Bond (Protein Donor)	false
N7	ND2	ASN- 134	3.26	139.62	H-Bond (Protein Donor)	false
N1	OD1	ASP- 137	2.79	173.28	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 137	2.94	158.8	H-Bond (Ligand Donor)	false
O6	N	LYS- 166	3.13	163.72	H-Bond (Protein Donor)	false
O2G	MG	MG- 202	2.02	0	Metal Acceptor	false
O2B	MG	MG- 202	2.11	0	Metal Acceptor	false
O3G	O	HOH- 307	3.41	150.89	H-Bond (Protein Donor)	false
O2A	O	HOH- 310	2.7	179.96	H-Bond (Protein Donor)	false