scPDB - 4p9c entry

Protein Data Bank Entry:

PDB ID : 4p9c

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2014-04-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Deoxycytidylate deaminase
ID:	H6WFU3_9CAUD
AC:	H6WFU3
Organism:	Cyanophage S-TIM5
Reign:	Viruses
TaxID:	1137745
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
E	24 %
F	5 %
J	71 %

Ligand binding site composition:

B-Factor:	31.778
Number of residues:	21
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.354	715.500

% Hydrophobic	% Polar
37.26	62.74
According to VolSite

Ligand :

HET Code:	DCM
Formula:	C9H12N3O7P
Molecular weight:	305.181 g/mol
DrugBank ID:	-
Buried Surface Area:	46.6 %
Polar Surface area:	170.38 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
19.736	8.3815	-9.1885

Binding mode :

What is Poseview ?

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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
O2	N	TRP- 42	3.15	161.31	H-Bond (Protein Donor)	false
C2'	CE2	TRP- 42	3.64	0	Hydrophobic	false
O3'	O	THR- 45	2.72	143.46	H-Bond (Ligand Donor)	false
O5'	OG	SER- 47	2.87	148.51	H-Bond (Protein Donor)	false
O2P	OG	SER- 47	3.39	129.86	H-Bond (Protein Donor)	false
C1'	CB	ASN- 71	4.49	0	Hydrophobic	false
O3'	ND2	ASN- 71	3.33	133.71	H-Bond (Protein Donor)	false