scPDB - 4dtx entry

Protein Data Bank Entry:

PDB ID : 4dtx

Resolution :1.840 Å

Experimental Method : X-ray

Deposition Date : 2012-02-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA-directed DNA polymerase
ID:	DPOL_BPR69
AC:	Q38087
Organism:	Enterobacteria phage RB69
Reign:	Viruses
TaxID:	12353
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	24.194
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	CA CA

Cavity properties

Ligandability	Volume (Å3)
0.283	1096.875

% Hydrophobic	% Polar
31.38	68.62
According to VolSite

Ligand :

HET Code:	TTP
Formula:	C10H13N2O14P3
Molecular weight:	478.137 g/mol
DrugBank ID:	DB02452
Buried Surface Area:	50.08 %
Polar Surface area:	279.44 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
1.30841	8.69521	48.2877

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	N	SER- 414	2.87	165.14	H-Bond (Protein Donor)	false
O2B	N	LEU- 415	3.04	166.26	H-Bond (Protein Donor)	false
C4'	CB	LEU- 415	4.45	0	Hydrophobic	false
C4'	CD1	TYR- 416	4.41	0	Hydrophobic	false
C1'	CE2	TYR- 416	4.21	0	Hydrophobic	false
C2'	CG	TYR- 416	3.57	0	Hydrophobic	false
O3'	N	TYR- 416	2.93	175.34	H-Bond (Protein Donor)	false
O2G	NH1	ARG- 482	2.89	171.97	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 482	2.76	168.13	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 482	3.75	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 482	3.64	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 486	3.94	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 560	3.11	159.24	H-Bond (Protein Donor)	false
O3A	NZ	LYS- 560	3.01	130.23	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 560	3.4	146.55	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 560	3.11	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 560	3.4	0	Ionic (Protein Cationic)	false
O1B	ND2	ASN- 564	3.27	158.76	H-Bond (Protein Donor)	false
C2'	CB	ASN- 564	4.42	0	Hydrophobic	false
C4'	CG2	THR- 622	3.85	0	Hydrophobic	false
O2A	CA	CA- 1002	2.45	0	Metal Acceptor	false
O2B	CA	CA- 1002	2.23	0	Metal Acceptor	false
O1G	CA	CA- 1002	2.27	0	Metal Acceptor	false
O2A	CA	CA- 1003	2.6	0	Metal Acceptor	false