Chemical Components in the PDB

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BIS : Summary

Code

BIS

One-letter code

X

Molecule name

1,1,5,5-TETRAFLUOROPHOSPHOPENTYLPHOSPHONIC ACID ADENYLATE ESTER

Systematic names

ProgramVersionName
ACDLabs 10.04 5'-O-[(R)-hydroxy{[(R)-hydroxy(1,1,5,5-tetrafluoro-5-phosphonopentyl)phosphoryl]oxy}phosphoryl]adenosine
OpenEye OEToolkits 1.5.0 [5-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]-1,1,5,5-tetrafluoro-pentyl]phosphonic acid

Formula

C15 H22 F4 N5 O12 P3

Formal charge

0

Molecular weight

633.276 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 FC(F)(P(=O)(O)O)CCCC(F)(F)P(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C(F)(F)CCCC(F)(F)[P](O)(O)=O)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(C(CCCC(F)(F)P(=O)(O)O)(F)F)O)O)O)N
Canonical SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)C(F)(F)CCCC(F)(F)[P](O)(O)=O)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(C(CCCC(F)(F)P(=O)(O)O)(F)F)O)O)O)N

IUPAC InChI

InChI=1S/C15H22F4N5O12P3/c16-14(17,37(27,28)29)2-1-3-15(18,19)38(30,31)36-39(32,33)34-4-7-9(25)10(26)13(35-7)24-6-23-8-11(20)21-5-22-12(8)24/h5-7,9-10,13,25-26H,1-4H2,(H,30,31)(H,32,33)(H2,20,21,22)(H2,27,28,29)/t7-,9-,10-,13-/m1/s1

IUPAC InChI key

VWQBAZQMKBHYJA-QYVSTXNMSA-N
BIS

wwPDB Information

Atom count

61 (39 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



BIS : Atoms of Molecule

Total Number of Atoms: 61
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 PB P PB R N N 0 -2.363 0.912 -2.179
2 O2B O O2B N N N 0 -3.351 -0.292 -2.584
3 O3B O O3B N N N 0 -3.15 2.019 -1.592
4 PA P PA R N N 0 -2.126 -0.122 0.178
5 O1A O O1A N N N 0 -2.987 1.099 0.776
6 O2A O O2A N N N 0 -3.038 -1.214 -0.231
7 O3A O O3A N N N 0 -1.29 0.386 -1.1
8 O5' O O5* N N N 0 -1.11 -0.665 1.303
9 C5' C C5* N N N 0 -1.909 -1.099 2.405
10 C4' C C4* R N N 0 -0.999 -1.63 3.516
11 O4' O O4* N N N 0 -0.122 -0.585 3.989
12 C3' C C3* S N N 0 -1.834 -2.034 4.751
13 O3' O O3* N N N 0 -2.066 -3.444 4.759
14 C2' C C2* R N N 0 -0.952 -1.621 5.953
15 O2' O O2* N N N 0 -0.614 -2.764 6.741
16 N7 N N7 N Y N 0 1.02 2.18 6.788
17 C1' C C1* R N N 0 0.308 -1.014 5.299
18 N9 N N9 N Y N 0 0.786 0.129 6.079
19 C8 C C8 N Y N 0 0.395 1.426 5.931
20 C5 C C5 N Y N 0 1.846 1.416 7.543
21 C6 C C6 N Y N 0 2.749 1.672 8.588
22 N6 N N6 N N N 0 2.93 2.957 9.069
23 N1 N N1 N Y N 0 3.422 0.65 9.108
24 C11 C C11 N N N 0 -1.489 1.508 -3.664
25 C2 C C2 N Y N 0 3.256 -0.578 8.655
26 N3 N N3 N Y N 0 2.426 -0.864 7.674
27 C4 C C4 N Y N 0 1.71 0.091 7.093
28 F11 F F11 N N N 0 -2.422 1.964 -4.601
29 F12 F F12 N N N 0 -0.631 2.555 -3.311
30 C12 C C12 N N N 0 -0.675 0.363 -4.27
31 C13 C C13 N N N 0 0.057 0.863 -5.516
32 C14 C C14 N N N 0 0.871 -0.281 -6.123
33 C15 C C15 N N N 0 1.604 0.219 -7.369
34 F51 F F51 N N N 0 0.672 0.676 -8.307
35 F52 F F52 N N N 0 2.463 1.266 -7.017
36 PN P PN N N N 0 2.575 -1.144 -8.092
37 ON1 O ON1 N N N 0 3.648 -1.67 -7.013
38 ON2 O ON2 N N N 0 1.587 -2.349 -8.498
39 ON3 O ON3 N N N 0 3.284 -0.66 -9.297
40 HO2B H BHO2 N N N 0 -2.799 -0.991 -2.962
41 HO1A H AHO1 N N N 0 -2.357 1.787 1.03
42 H5'1 H 1H5* N N N 0 -2.581 -1.891 2.077
43 H5'2 H 2H5* N N N 0 -2.493 -0.26 2.784
44 H4' H H4* N N N 0 -0.418 -2.479 3.156
45 H3' H H3* N N N 0 -2.78 -1.492 4.766
46 HO'3 H 3HO* N N N 0 -2.589 -3.636 5.549
47 H2' H H2* N N N 0 -1.462 -0.875 6.562
48 HO'2 H 2HO* N N N 0 -1.446 -3.132 7.07
49 H1' H H1* N N N 0 1.091 -1.768 5.213
50 H8 H H8 N N N 0 -0.327 1.777 5.209
51 H121 H 1H12 N N N 0 0.05 0.007 -3.54
52 HN61 H 1HN6 N N N 0 3.553 3.12 9.794
53 HN62 H 2HN6 N N N 0 2.435 3.694 8.679
54 H2 H H2 N N N 0 3.824 -1.379 9.106
55 H122 H 2H12 N N N 0 -1.344 -0.452 -4.545
56 H131 H 1H13 N N N 0 -0.668 1.219 -6.247
57 H132 H 2H13 N N N 0 0.726 1.679 -5.242
58 H141 H 1H14 N N N 0 1.598 -0.637 -5.392
59 H142 H 2H14 N N N 0 0.203 -1.096 -6.398
60 HO1 H HO1 N N N 0 4.138 -2.389 -7.434
61 HO2 H HO2 N N N 0 1.146 -2.634 -7.686



BIS : Chemical Bonds

Total Number of Bonds: 63
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 PB O2B P O sing 1.61 N N
2 PB O3B P O doub 1.48 N N
3 PB O3A P O sing 1.61 N N
4 PB C11 P C sing 1.82 N N
5 O2B HO2B O H sing 0.97 N N
6 PA O1A P O sing 1.61 N N
7 PA O2A P O doub 1.48 N N
8 PA O3A P O sing 1.61 N N
9 PA O5' P O sing 1.61 N N
10 O1A HO1A O H sing 0.97 N N
11 O5' C5' O C sing 1.43 N N
12 C5' C4' C C sing 1.53 N N
13 C5' H5'1 C H sing 1.09 N N
14 C5' H5'2 C H sing 1.09 N N
15 C4' O4' C O sing 1.44 N N
16 C4' C3' C C sing 1.54 N N
17 C4' H4' C H sing 1.09 N N
18 O4' C1' O C sing 1.44 N N
19 C3' O3' C O sing 1.43 N N
20 C3' C2' C C sing 1.55 N N
21 C3' H3' C H sing 1.09 N N
22 O3' HO'3 O H sing 0.97 N N
23 C2' O2' C O sing 1.43 N N
24 C2' C1' C C sing 1.54 N N
25 C2' H2' C H sing 1.09 N N
26 O2' HO'2 O H sing 0.97 N N
27 C1' N9 C N sing 1.46 N N
28 C1' H1' C H sing 1.09 N N
29 N9 C8 N C sing 1.36 N Y
30 N9 C4 N C sing 1.37 N Y
31 C8 N7 C N doub 1.3 N Y
32 C8 H8 C H sing 1.08 N N
33 N7 C5 N C sing 1.35 N Y
34 C5 C6 C C sing 1.4 N Y
35 C5 C4 C C doub 1.41 N Y
36 C6 N6 C N sing 1.38 N N
37 C6 N1 C N doub 1.33 N Y
38 N6 HN61 N H sing 0.97 N N
39 N6 HN62 N H sing 0.97 N N
40 N1 C2 N C sing 1.32 N Y
41 C2 N3 C N doub 1.32 N Y
42 C2 H2 C H sing 1.08 N N
43 N3 C4 N C sing 1.33 N Y
44 C11 F11 C F sing 1.4 N N
45 C11 F12 C F sing 1.4 N N
46 C11 C12 C C sing 1.53 N N
47 C12 C13 C C sing 1.53 N N
48 C12 H121 C H sing 1.09 N N
49 C12 H122 C H sing 1.09 N N
50 C13 C14 C C sing 1.53 N N
51 C13 H131 C H sing 1.09 N N
52 C13 H132 C H sing 1.09 N N
53 C14 C15 C C sing 1.53 N N
54 C14 H141 C H sing 1.09 N N
55 C14 H142 C H sing 1.09 N N
56 C15 F51 C F sing 1.4 N N
57 C15 F52 C F sing 1.4 N N
58 C15 PN C P sing 1.82 N N
59 PN ON1 P O sing 1.61 N N
60 PN ON2 P O sing 1.61 N N
61 PN ON3 P O doub 1.48 N N
62 ON1 HO1 O H sing 0.97 N N
63 ON2 HO2 O H sing 0.97 N N



BIS : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
BIS 16pk Open in New Window Bound ligand 1 1