scPDB - 1zbd entry

Protein Data Bank Entry:

PDB ID : 1zbd

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 1998-11-06

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-3A
ID:	RAB3A_RAT
AC:	P63012
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	49.620
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.232	455.625

% Hydrophobic	% Polar
48.15	51.85
According to VolSite

Ligand :

HET Code:	GTP
Formula:	C10H12N5O14P3
Molecular weight:	519.149 g/mol
DrugBank ID:	DB04137
Buried Surface Area:	79.36 %
Polar Surface area:	335.56 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	4
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
9.41956	17.8602	4.29741

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
O2G	OG	SER- 31	2.64	158.71	H-Bond (Protein Donor)	false
O3B	N	SER- 32	3.25	162.97	H-Bond (Protein Donor)	false
C5'	CB	SER- 32	4.42	0	Hydrophobic	false
O1B	N	GLY- 34	3.4	153.55	H-Bond (Protein Donor)	false
O3A	N	GLY- 34	2.99	122.33	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 35	2.64	147.81	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 35	2.73	142.49	H-Bond (Protein Donor)	false
O1B	N	LYS- 35	3.43	174.96	H-Bond (Protein Donor)	false
O3A	N	LYS- 35	3.4	124.54	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 35	2.64	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 35	2.73	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 35	3.92	0	Ionic (Protein Cationic)	false
O2B	N	THR- 36	2.91	170.13	H-Bond (Protein Donor)	false
O1A	N	SER- 37	2.81	155.19	H-Bond (Protein Donor)	false
O1A	OG	SER- 37	2.6	163.43	H-Bond (Protein Donor)	false
C2'	CE1	PHE- 47	3.91	0	Hydrophobic	false
C1'	CZ	PHE- 47	4.23	0	Hydrophobic	false
O2'	O	THR- 48	3.25	154.99	H-Bond (Ligand Donor)	false
O3'	O	PRO- 49	3.07	159.75	H-Bond (Ligand Donor)	false
C5'	CD1	PHE- 51	3.85	0	Hydrophobic	false
C3'	CB	PHE- 51	4.21	0	Hydrophobic	false
O2G	OG	SER- 53	2.8	167.33	H-Bond (Protein Donor)	false
O3G	N	THR- 54	2.99	158.59	H-Bond (Protein Donor)	false
O1G	N	GLY- 80	3.01	142.49	H-Bond (Protein Donor)	false
N7	ND2	ASN- 135	3.16	142.55	H-Bond (Protein Donor)	false
N1	OD2	ASP- 138	3.37	133.26	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 138	2.91	165.46	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 138	2.82	157.97	H-Bond (Ligand Donor)	false
O6	OG	SER- 165	2.99	163.62	H-Bond (Protein Donor)	false
O6	N	ALA- 166	2.69	121.06	H-Bond (Protein Donor)	false
O6	N	LYS- 167	3.24	146.81	H-Bond (Protein Donor)	false
O3G	MG	MG- 302	2.42	0	Metal Acceptor	false
O2B	MG	MG- 302	2.59	0	Metal Acceptor	false