scPDB - 2d4h entry

Protein Data Bank Entry:

PDB ID : 2d4h

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2005-10-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Guanylate-binding protein 1
ID:	GBP1_HUMAN
AC:	P32455
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.063
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.352	624.375

% Hydrophobic	% Polar
36.22	63.78
According to VolSite

Ligand :

HET Code:	5GP
Formula:	C10H12N5O8P
Molecular weight:	361.205 g/mol
DrugBank ID:	-
Buried Surface Area:	60.9 %
Polar Surface area:	217.22 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-3.6235	50.0116	-4.07542

Binding mode :

What is Poseview ?

2D View
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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
O2P	N	ARG- 48	3.34	145.95	H-Bond (Protein Donor)	false
C4'	CB	ARG- 48	4.24	0	Hydrophobic	false
O3P	N	THR- 49	2.82	139.27	H-Bond (Protein Donor)	false
O3P	N	GLY- 50	2.92	125.08	H-Bond (Protein Donor)	false
O2P	NZ	LYS- 51	3.73	0	Ionic (Protein Cationic)	false
O3P	NZ	LYS- 51	3.34	0	Ionic (Protein Cationic)	false
O3P	NZ	LYS- 51	3.34	155.63	H-Bond (Protein Donor)	false
O3P	N	LYS- 51	2.87	165.59	H-Bond (Protein Donor)	false
O1P	N	SER- 52	2.73	143.17	H-Bond (Protein Donor)	false
C2'	CZ	PHE- 65	4.41	0	Hydrophobic	false
O3'	O	GLY- 68	3.25	174.43	H-Bond (Ligand Donor)	false
N7	NH2	ARG- 183	2.69	122.08	H-Bond (Protein Donor)	false
O6	NH2	ARG- 183	2.89	140.54	H-Bond (Protein Donor)	false
O6	NE	ARG- 183	2.77	150.48	H-Bond (Protein Donor)	false
N1	OD2	ASP- 184	2.85	133.95	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 184	2.72	123.54	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 184	2.69	143.72	H-Bond (Ligand Donor)	false
O6	O	HOH- 640	2.8	179.97	H-Bond (Protein Donor)	false