scPDB - 4i1v entry

Protein Data Bank Entry:

PDB ID : 4i1v

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2012-11-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dephospho-CoA kinase
ID:	A4JBA9_BURVG
AC:	A4JBA9
Organism:	Burkholderia vietnamiensis )
Reign:	Bacteria
TaxID:	269482
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	47.200
Number of residues:	23
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.255	324.000

% Hydrophobic	% Polar
44.79	55.21
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	54.34 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
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
64.7276	23.302	-25.3384

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
O3B	N	GLY- 11	3.23	135.34	H-Bond (Protein Donor)	false
O2B	N	GLY- 13	3.27	162.58	H-Bond (Protein Donor)	false
O2B	N	LYS- 14	3.09	146.97	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 14	2.58	176.39	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 14	2.58	0	Ionic (Protein Cationic)	false
O1B	N	THR- 15	2.96	163.83	H-Bond (Protein Donor)	false
O1B	OG1	THR- 15	2.69	155.44	H-Bond (Protein Donor)	false
O2A	OG1	THR- 15	3.32	121.81	H-Bond (Protein Donor)	false
O1A	N	THR- 16	3.01	147.98	H-Bond (Protein Donor)	false
C1'	CD	ARG- 140	4.45	0	Hydrophobic	false
C5'	CD	ARG- 140	3.88	0	Hydrophobic	false
N7	ND2	ASN- 175	3	161.99	H-Bond (Protein Donor)	false
N6	OD1	ASN- 175	2.79	152.69	H-Bond (Ligand Donor)	false
N6	O	THR- 179	3.35	140.31	H-Bond (Ligand Donor)	false