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VA5 : Summary
Code ![](/pdbe/static/images/help.png)
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VA5
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One-letter code ![](/pdbe/static/images/help.png)
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X
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Molecule name ![](/pdbe/static/images/help.png)
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9-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-D-threo-pentofuranosyl}-9H-purin-6-amine
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Systematic names ![](/pdbe/static/images/help.png)
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Formula ![](/pdbe/static/images/help.png)
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C11 H16 Cl F N5 O11 P3
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Formal charge ![](/pdbe/static/images/help.png)
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0
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Molecular weight ![](/pdbe/static/images/help.png)
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541.644 Da
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SMILES ![](/pdbe/static/images/help.png)
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Type | Program | Version | Descriptor |
SMILES
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ACDLabs |
12.01 |
P(=O)(O)(OP(O)(C(Cl)(P(O)(O)=O)F)=O)OCC3OC(n1cnc2c1ncnc2N)CC3O |
SMILES
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CACTVS |
3.385 |
Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[C](F)(Cl)[P](O)(O)=O)O3 |
SMILES
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OpenEye OEToolkits |
2.0.6 |
c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(C(F)(P(=O)(O)O)Cl)O)O)N |
Canonical SMILES
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CACTVS |
3.385 |
Nc1ncnc2n(cnc12)[C@@H]3C[C@@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)[C@@](F)(Cl)[P](O)(O)=O)O3 |
Canonical SMILES
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OpenEye OEToolkits |
2.0.6 |
c1nc(c2c(n1)n(cn2)[C@@H]3C[C@H]([C@H](O3)COP(=O)(O)OP(=O)([C@](F)(P(=O)(O)O)Cl)O)O)N |
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IUPAC InChI ![](/pdbe/static/images/help.png) | InChI=1S/C11H16ClFN5O11P3/c12-11(13,30(20,21)22)31(23,24)29-32(25,26)27-2-6-5(19)1-7(28-6)18-4-17-8-9(14)15-3-16-10(8)18/h3-7,19H,1-2H2,(H,23,24)(H,25,26)(H2,14,15,16)(H2,20,21,22)/t5-,6-,7+,11-/m1/s1 |
IUPAC InChI key ![](/pdbe/static/images/help.png) | MGXOAMBWOAGILL-FHZUQPTBSA-N |
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wwPDB Information |
Atom count ![](/pdbe/static/images/help.png)
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48 (32 without Hydrogen)
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Polymer type ![](/pdbe/static/images/help.png)
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Bound ligand
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Type description ![](/pdbe/static/images/help.png)
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NON-POLYMER
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Type code ![](/pdbe/static/images/help.png)
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HETAIN
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Is modified ![](/pdbe/static/images/help.png)
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No
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Standard parent ![](/pdbe/static/images/help.png)
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Not Assigned
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Defined at ![](/pdbe/static/images/help.png)
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2018-03-22
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Last modified at ![](/pdbe/static/images/help.png)
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2018-06-29
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Status ![](/pdbe/static/images/help.png)
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Released
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Obsoleted ![](/pdbe/static/images/help.png)
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Not Assigned
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VA5 : Atoms of Molecule
Total Number of Atoms: 48
Record |
Atom Name |
Symbol |
PDB Name |
Stereochemistry |
Is Aromatic |
Is Leaving Atom |
Charge |
X-Coordinate |
Y-Coordinate |
Z-Coordinate |
1 |
PA |
P |
P1 |
N |
N |
N |
0 |
1.356 |
-1.793 |
-0.485 |
2 |
O1A |
O |
O1 |
N |
N |
N |
0 |
1.054 |
-1.907 |
-2.062 |
3 |
O2A |
O |
O2 |
N |
N |
N |
0 |
1.934 |
-3.066 |
0.0 |
4 |
O3A |
O |
O3 |
N |
N |
N |
0 |
2.401 |
-0.596 |
-0.225 |
5 |
O5' |
O |
O4 |
N |
N |
N |
0 |
-0.014 |
-1.49 |
0.304 |
6 |
PB |
P |
P2 |
N |
N |
N |
0 |
3.987 |
-0.427 |
-0.449 |
7 |
O2B |
O |
O5 |
N |
N |
N |
0 |
4.303 |
-0.605 |
-1.884 |
8 |
O1B |
O |
O6 |
N |
N |
N |
0 |
4.773 |
-1.534 |
0.416 |
9 |
C3B |
C |
C1 |
S |
N |
N |
0 |
4.501 |
1.239 |
0.084 |
10 |
F3B |
F |
F1 |
N |
N |
N |
0 |
3.819 |
2.201 |
-0.667 |
11 |
CL1 |
CL |
CL1 |
N |
N |
N |
0 |
4.115 |
1.456 |
1.832 |
12 |
PG |
P |
P3 |
N |
N |
N |
0 |
6.296 |
1.431 |
-0.17 |
13 |
O1G |
O |
O7 |
N |
N |
N |
0 |
6.751 |
2.901 |
0.301 |
14 |
O2G |
O |
O8 |
N |
N |
N |
0 |
7.082 |
0.323 |
0.695 |
15 |
O3G |
O |
O9 |
N |
N |
N |
0 |
6.613 |
1.252 |
-1.605 |
16 |
C5' |
C |
C2 |
N |
N |
N |
0 |
-1.102 |
-2.415 |
0.357 |
17 |
C4' |
C |
C3 |
R |
N |
N |
0 |
-2.241 |
-1.815 |
1.184 |
18 |
O4' |
O |
O10 |
N |
N |
N |
0 |
-2.789 |
-0.68 |
0.505 |
19 |
C1' |
C |
C4 |
S |
N |
N |
0 |
-4.168 |
-0.919 |
0.183 |
20 |
N9 |
N |
N1 |
N |
Y |
N |
0 |
-4.945 |
0.315 |
0.32 |
21 |
C4 |
C |
C5 |
N |
Y |
N |
0 |
-6.135 |
0.599 |
-0.299 |
22 |
N3 |
N |
N2 |
N |
Y |
N |
0 |
-6.93 |
-0.047 |
-1.146 |
23 |
C2 |
C |
C6 |
N |
Y |
N |
0 |
-8.044 |
0.506 |
-1.577 |
24 |
N1 |
N |
N3 |
N |
Y |
N |
0 |
-8.427 |
1.713 |
-1.201 |
25 |
C6 |
C |
C7 |
N |
Y |
N |
0 |
-7.697 |
2.435 |
-0.357 |
26 |
N6 |
N |
N4 |
N |
N |
N |
0 |
-8.107 |
3.699 |
0.032 |
27 |
C5 |
C |
C8 |
N |
Y |
N |
0 |
-6.499 |
1.886 |
0.131 |
28 |
N7 |
N |
N5 |
N |
Y |
N |
0 |
-5.53 |
2.313 |
0.976 |
29 |
C8 |
C |
C9 |
N |
Y |
N |
0 |
-4.62 |
1.391 |
1.092 |
30 |
C2' |
C |
C10 |
N |
N |
N |
0 |
-4.647 |
-1.975 |
1.212 |
31 |
C3' |
C |
C11 |
R |
N |
N |
0 |
-3.372 |
-2.854 |
1.349 |
32 |
O3' |
O |
O11 |
N |
N |
N |
0 |
-3.315 |
-3.834 |
0.311 |
33 |
H1 |
H |
H1 |
N |
N |
N |
0 |
0.673 |
-1.106 |
-2.448 |
34 |
H2 |
H |
H2 |
N |
N |
N |
0 |
4.611 |
-1.477 |
1.367 |
35 |
H3 |
H |
H3 |
N |
N |
N |
0 |
7.696 |
3.074 |
0.194 |
36 |
H4 |
H |
H4 |
N |
N |
N |
0 |
6.921 |
0.38 |
1.647 |
37 |
H5 |
H |
H5 |
N |
N |
N |
0 |
-1.455 |
-2.619 |
-0.654 |
38 |
H6 |
H |
H6 |
N |
N |
N |
0 |
-0.767 |
-3.344 |
0.819 |
39 |
H7 |
H |
H7 |
N |
N |
N |
0 |
-1.868 |
-1.516 |
2.164 |
40 |
H8 |
H |
H8 |
N |
N |
N |
0 |
-4.258 |
-1.311 |
-0.83 |
41 |
H9 |
H |
H9 |
N |
N |
N |
0 |
-8.667 |
-0.046 |
-2.264 |
42 |
H10 |
H |
H10 |
N |
N |
N |
0 |
-8.936 |
4.067 |
-0.312 |
43 |
H11 |
H |
H11 |
N |
N |
N |
0 |
-7.565 |
4.216 |
0.648 |
44 |
H12 |
H |
H12 |
N |
N |
N |
0 |
-3.736 |
1.467 |
1.708 |
45 |
H13 |
H |
H13 |
N |
N |
N |
0 |
-4.905 |
-1.507 |
2.161 |
46 |
H14 |
H |
H14 |
N |
N |
N |
0 |
-5.483 |
-2.555 |
0.821 |
47 |
H15 |
H |
H15 |
N |
N |
N |
0 |
-3.33 |
-3.327 |
2.33 |
48 |
H16 |
H |
H16 |
N |
N |
N |
0 |
-4.055 |
-4.456 |
0.317 |
VA5 : Chemical Bonds
Total Number of Bonds: 50
VA5 : Used in PDB Entries
Total Number of PDB Entries: 1
Ligand Code |
PDB Entry ID |
Type |
Total |
Distinct |
VA5 |
6cr9 ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724459988286) |
Bound ligand
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1 |
1 |
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