scPDB - 4g5q entry

Protein Data Bank Entry:

PDB ID : 4g5q

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2012-07-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Guanine nucleotide-binding protein G(i) subunit alpha-1
ID:	GNAI1_HUMAN
AC:	P63096
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	89 %
F	11 %

Ligand binding site composition:

B-Factor:	49.604
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.761	894.375

% Hydrophobic	% Polar
39.25	60.75
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	86.39 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
76.9667	-20.3704	52.1035

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
O1B	N	GLU- 43	2.6	149.52	H-Bond (Protein Donor)	false
C5'	CB	GLU- 43	4.32	0	Hydrophobic	false
O2B	N	GLY- 45	3.17	143.65	H-Bond (Protein Donor)	false
O3A	N	GLY- 45	3.02	130.81	H-Bond (Protein Donor)	false
O2B	N	LYS- 46	2.89	139.92	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 46	2.7	150.73	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 46	2.7	0	Ionic (Protein Cationic)	false
O3B	N	SER- 47	2.77	159.06	H-Bond (Protein Donor)	false
O3B	OG	SER- 47	3.03	136.59	H-Bond (Protein Donor)	false
O1A	OG	SER- 47	3.09	140.56	H-Bond (Protein Donor)	false
O2A	OG1	THR- 48	2.65	172.32	H-Bond (Protein Donor)	false
O2A	N	THR- 48	2.79	142.75	H-Bond (Protein Donor)	false
C4'	CB	ASP- 150	4.24	0	Hydrophobic	false
C1'	CB	ASP- 150	3.94	0	Hydrophobic	false
O3'	OG	SER- 151	2.83	149.86	H-Bond (Ligand Donor)	false
O2'	NH1	ARG- 176	3.04	146.04	H-Bond (Protein Donor)	false
N3	NH1	ARG- 176	3.16	128.2	H-Bond (Protein Donor)	false
O3'	NE	ARG- 178	3.2	170.13	H-Bond (Protein Donor)	false
N7	ND2	ASN- 269	3.01	153.41	H-Bond (Protein Donor)	false
O4'	NZ	LYS- 270	2.97	174.3	H-Bond (Protein Donor)	false
O6	N	LYS- 270	3.16	123.32	H-Bond (Protein Donor)	false
N1	OD2	ASP- 272	3.44	132.53	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 272	2.82	153.69	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 272	2.83	166.61	H-Bond (Ligand Donor)	false
O6	N	ALA- 326	2.93	132.25	H-Bond (Protein Donor)	false
C1'	CG2	THR- 327	4.45	0	Hydrophobic	false
O1B	CZ	ARG- 635	3.68	0	Ionic (Protein Cationic)	false
O3B	CZ	ARG- 635	3.75	0	Ionic (Protein Cationic)	false
O1B	NE	ARG- 635	2.95	162.31	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 635	2.84	160.62	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 640	2.71	154.42	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 640	3.63	0	Ionic (Protein Cationic)	false