scPDB - 3vth entry

Protein Data Bank Entry:

PDB ID : 3vth

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2012-05-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Carbamoyltransferase
ID:	Q8RDB0_CALS4
AC:	Q8RDB0
Organism:	Caldanaerobacter subterraneus subsp. tengcongensis
Reign:	Bacteria
TaxID:	273068
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.102
Number of residues:	44
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	FE

Cavity properties

Ligandability	Volume (Å3)
0.341	2156.625

% Hydrophobic	% Polar
43.97	56.03
According to VolSite

Ligand :

HET Code:	AP2
Formula:	C11H14N5O9P2
Molecular weight:	422.204 g/mol
DrugBank ID:	DB03148
Buried Surface Area:	75.59 %
Polar Surface area:	251.48 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
90.9627	0.480148	-13.6424

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
C3A	CD2	TYR- 409	3.86	0	Hydrophobic	false
O1B	N	GLY- 508	2.78	121.2	H-Bond (Protein Donor)	false
O1B	N	THR- 509	2.65	159.39	H-Bond (Protein Donor)	false
O3B	OG1	THR- 509	3.14	143.17	H-Bond (Protein Donor)	false
C3'	CG	GLU- 617	4.37	0	Hydrophobic	false
N6	OE1	GLU- 625	2.82	146.26	H-Bond (Ligand Donor)	false
O2A	N	GLY- 702	3.16	140.09	H-Bond (Protein Donor)	false
N1	ND2	ASN- 706	2.92	151.57	H-Bond (Protein Donor)	false
C3A	CB	ASP- 734	4.19	0	Hydrophobic	false
O1A	N	ASP- 734	3	148.6	H-Bond (Protein Donor)	false
O2B	FE	FE- 807	1.96	0	Metal Acceptor	false
O2A	FE	FE- 807	2.22	0	Metal Acceptor	false