scPDB - 1vh3 entry

Protein Data Bank Entry:

PDB ID : 1vh3

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2003-12-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-deoxy-manno-octulosonate cytidylyltransferase
ID:	KDSB_HAEIN
AC:	P44490
Organism:	Haemophilus influenzae
Reign:	Bacteria
TaxID:	71421
EC Number:	2.7.7.38

Chains:

Chain Name:	Percentage of Residues within binding site
A	2 %
B	98 %

Ligand binding site composition:

B-Factor:	45.767
Number of residues:	44
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.321	813.375

% Hydrophobic	% Polar
28.63	71.37
According to VolSite

Ligand :

HET Code:	CMK
Formula:	C17H24N3O15P
Molecular weight:	541.357 g/mol
DrugBank ID:	DB04482
Buried Surface Area:	64.04 %
Polar Surface area:	307.05 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
66.2459	4.08481	4.12906

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
C1'	CB	PRO- 8	3.6	0	Hydrophobic	false
O2'	O	PRO- 8	2.89	143.57	H-Bond (Ligand Donor)	false
O2'	N	ARG- 10	3.01	155.12	H-Bond (Protein Donor)	false
N4C	O	HIS- 72	3.13	145.53	H-Bond (Ligand Donor)	false
N3C	NH2	ARG- 78	3.35	157.53	H-Bond (Protein Donor)	false
O2C	NE	ARG- 78	2.86	148.71	H-Bond (Protein Donor)	false
C3'	CB	GLN- 98	4.11	0	Hydrophobic	false
C4'	CG	GLN- 98	3.46	0	Hydrophobic	false
O5	NE2	GLN- 98	2.8	142.83	H-Bond (Protein Donor)	false
O3'	N	GLY- 99	2.64	131.56	H-Bond (Protein Donor)	false
C7	CG2	VAL- 142	3.65	0	Hydrophobic	false
C7	CB	HIS- 185	4.45	0	Hydrophobic	false
C5	CZ	TYR- 189	4.47	0	Hydrophobic	false
O5	OH	TYR- 189	2.76	155.89	H-Bond (Ligand Donor)	false
C6	CD1	LEU- 213	3.75	0	Hydrophobic	false
C4	CG	GLU- 214	4.44	0	Hydrophobic	false
O4	N	GLU- 214	2.75	163.19	H-Bond (Protein Donor)	false
O4	OE2	GLU- 214	2.6	138.31	H-Bond (Ligand Donor)	false
O7	NE2	GLN- 215	3.23	129.6	H-Bond (Protein Donor)	false
O4'	O	HOH- 287	2.98	179.98	H-Bond (Protein Donor)	false