scPDB - 2ggs entry

Protein Data Bank Entry:

PDB ID : 2ggs

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2006-03-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	dTDP-4-dehydrorhamnose reductase
ID:	Q96Z61_SULTO
AC:	Q96Z61
Organism:	Sulfolobus tokodaii
Reign:	Archaea
TaxID:	273063
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.823
Number of residues:	51
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.860	799.875

% Hydrophobic	% Polar
40.08	59.92
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	70.51 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-8.26112	33.0244	29.3496

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
O3B	OG	SER- 9	2.85	164.12	H-Bond (Ligand Donor)	false
O1X	OG	SER- 9	2.59	144.71	H-Bond (Protein Donor)	false
O2A	N	GLN- 11	3.01	158.54	H-Bond (Protein Donor)	false
O2N	NE2	GLN- 11	2.91	160.8	H-Bond (Protein Donor)	false
O1N	N	LEU- 12	3.01	175.62	H-Bond (Protein Donor)	false
C5D	CB	LEU- 12	4.09	0	Hydrophobic	false
O1X	N	ASN- 31	2.97	168.58	H-Bond (Protein Donor)	false
O3X	N	SER- 32	2.84	155.53	H-Bond (Protein Donor)	false
O1X	N	SER- 33	2.9	156.25	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 42	3.04	164.26	H-Bond (Ligand Donor)	false
N1A	N	LEU- 43	2.9	168.91	H-Bond (Protein Donor)	false
C5D	CB	ALA- 64	4.34	0	Hydrophobic	false
C1B	CB	ALA- 65	3.89	0	Hydrophobic	false
O4B	N	ALA- 66	3.05	159.57	H-Bond (Protein Donor)	false
C3D	CB	ALA- 66	3.73	0	Hydrophobic	false
O1A	OG1	THR- 68	2.86	146.31	H-Bond (Protein Donor)	false
C2D	CG2	THR- 68	3.66	0	Hydrophobic	false
C4D	CG2	ILE- 105	3.74	0	Hydrophobic	false
C5N	CB	THR- 107	3.76	0	Hydrophobic	false
O2D	OH	TYR- 130	2.76	143.76	H-Bond (Protein Donor)	false
O3D	NZ	LYS- 134	2.87	144.63	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 134	3.17	134.11	H-Bond (Protein Donor)	false
C5N	CG2	THR- 151	3.81	0	Hydrophobic	false
C5D	CD1	ILE- 154	3.81	0	Hydrophobic	false
C3N	CG1	ILE- 154	3.92	0	Hydrophobic	false
O1A	NZ	LYS- 158	2.78	161.63	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 158	2.78	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 158	3.71	0	Ionic (Protein Cationic)	false
O1N	O	HOH- 914	2.79	144.47	H-Bond (Protein Donor)	false
O1A	O	HOH- 988	3.11	179.97	H-Bond (Protein Donor)	false