scPDB - 4tqg entry

Protein Data Bank Entry:

PDB ID : 4tqg

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2014-06-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative dTDP-d-glucose 4 6-dehydratase
ID:	G5CSR9_9VIRU
AC:	G5CSR9
Organism:	Megavirus chiliensis
Reign:	Viruses
TaxID:	1094892
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.443
Number of residues:	47
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.459	475.875

% Hydrophobic	% Polar
30.50	69.50
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	69.51 %
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
67.7751	18.9889	9.78502

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
O3B	N	SER- 14	3.11	142.49	H-Bond (Protein Donor)	false
O3B	OG	SER- 14	2.55	146.63	H-Bond (Ligand Donor)	false
O2A	N	SER- 16	3.31	160.9	H-Bond (Protein Donor)	false
O2N	N	LEU- 17	2.96	160.34	H-Bond (Protein Donor)	false
C4D	CD2	LEU- 17	4.08	0	Hydrophobic	false
O1X	NH2	ARG- 36	3.43	171.78	H-Bond (Protein Donor)	false
O2X	N	ARG- 36	2.89	155	H-Bond (Protein Donor)	false
O2X	NE	ARG- 36	2.93	153.11	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 36	3.84	0	Ionic (Protein Cationic)	false
O3X	N	ASP- 37	2.86	142.68	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 40	3.68	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 40	3.59	0	Ionic (Protein Cationic)	false
N6A	OD1	ASP- 59	2.81	157.35	H-Bond (Ligand Donor)	false
N1A	N	ILE- 60	2.92	175.06	H-Bond (Protein Donor)	false
C4D	CB	ALA- 81	3.93	0	Hydrophobic	false
C1B	CB	ALA- 82	4.17	0	Hydrophobic	false
C3D	CB	ALA- 83	4.27	0	Hydrophobic	false
N6A	OG1	THR- 100	3.39	127.79	H-Bond (Ligand Donor)	false
C4D	CG1	VAL- 128	4	0	Hydrophobic	false
O3D	O	VAL- 128	3.44	131.17	H-Bond (Ligand Donor)	false
C5N	CB	THR- 130	4.07	0	Hydrophobic	false
O3D	NZ	LYS- 144	3.04	129.95	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 144	3.07	127.67	H-Bond (Protein Donor)	false
O7N	ND2	ASN- 170	3.08	138.23	H-Bond (Protein Donor)	false
O7N	N	VAL- 171	2.93	171.03	H-Bond (Protein Donor)	false
C3N	CG1	VAL- 171	4.29	0	Hydrophobic	false
O2N	O	HOH- 560	3.03	149.69	H-Bond (Protein Donor)	false