Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

V3A : Summary

Code

V3A

One-letter code

X

Molecule name

9-{2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 9-{2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine
OpenEye OEToolkits 2.0.6 [(~{R})-[[[(2~{R},3~{S},5~{S})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-fluoranyl-methyl]phosphonic acid

Formula

C11 H17 F N5 O11 P3

Formal charge

0

Molecular weight

507.199 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 P(=O)(O)(OP(O)(C(P(=O)(O)O)F)=O)OCC3OC(n1cnc2c1ncnc2N)CC3O
SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[CH](F)[P](O)(O)=O)O3
SMILES OpenEye OEToolkits 2.0.6 c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(C(F)P(=O)(O)O)O)O)N
Canonical SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[C@@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)[C@H](F)[P](O)(O)=O)O3
Canonical SMILES OpenEye OEToolkits 2.0.6 c1nc(c2c(n1)n(cn2)[C@@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)([C@H](F)P(=O)(O)O)O)O)N

IUPAC InChI

InChI=1S/C11H17FN5O11P3/c12-11(29(19,20)21)30(22,23)28-31(24,25)26-2-6-5(18)1-7(27-6)17-4-16-8-9(13)14-3-15-10(8)17/h3-7,11,18H,1-2H2,(H,22,23)(H,24,25)(H2,13,14,15)(H2,19,20,21)/t5-,6+,7-,11+/m0/s1

IUPAC InChI key

AHVBRAYGASDMPK-QMWPFBOUSA-N
V3A

wwPDB Information

Atom count

48 (31 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-03-22

Last modified at

2018-06-29

Status

Released

Obsoleted

Not Assigned



V3A : 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 1.685 -1.585 -0.661
2 O1A O O1 N N N 0 1.441 -1.411 -2.243
3 O2A O O2 N N N 0 2.269 -2.918 -0.395
4 O3A O O3 N N N 0 2.696 -0.443 -0.146
5 O5' O O4 N N N 0 0.281 -1.448 0.116
6 PB P P2 N N N 0 4.285 -0.216 -0.274
7 O2B O O5 N N N 0 4.657 -0.125 -1.704
8 O1B O O6 N N N 0 5.061 -1.454 0.404
9 C3B C C1 R N N 0 4.748 1.329 0.574
10 F3B F F1 N N N 0 4.075 2.405 -0.015
11 PG P P3 N N N 0 6.548 1.587 0.429
12 O1G O O7 N N N 0 6.952 1.686 -1.126
13 O2G O O8 N N N 0 6.957 2.952 1.178
14 O3G O O9 N N N 0 7.26 0.449 1.052
15 C5' C C2 N N N 0 -0.79 -2.381 -0.043
16 N9 N N1 N Y N 0 -4.681 0.263 0.27
17 C4' C C3 R N N 0 -1.969 -1.957 0.835
18 O4' O O10 N N N 0 -2.514 -0.723 0.353
19 C1' C C4 S N N 0 -3.876 -0.916 -0.06
20 C4 C C5 N Y N 0 -5.853 0.641 -0.334
21 N3 N N2 N Y N 0 -6.605 0.151 -1.314
22 C2 C C6 N Y N 0 -7.713 0.761 -1.679
23 N1 N N3 N Y N 0 -8.132 1.873 -1.105
24 C6 C C7 N Y N 0 -7.447 2.437 -0.116
25 N6 N N4 N N N 0 -7.895 3.603 0.481
26 C5 C C8 N Y N 0 -6.257 1.823 0.31
27 N7 N N5 N Y N 0 -5.327 2.1 1.256
28 C8 C C9 N Y N 0 -4.404 1.183 1.237
29 C2' C C10 N N N 0 -4.371 -2.148 0.739
30 C3' C C11 S N N 0 -3.085 -3.021 0.763
31 O3' O O11 N N N 0 -3.064 -3.863 1.917
32 H1 H H1 N N N 0 1.059 -0.558 -2.491
33 H2 H H2 N N N 0 4.864 -1.574 1.343
34 H3 H H3 N N N 0 4.475 1.262 1.627
35 H4 H H4 N N N 0 6.521 2.411 -1.599
36 H5 H H5 N N N 0 7.902 3.152 1.141
37 H6 H H6 N N N 0 -1.103 -2.4 -1.087
38 H7 H H7 N N N 0 -0.454 -3.374 0.254
39 H8 H H8 N N N 0 -1.638 -1.837 1.866
40 H9 H H9 N N N 0 -3.922 -1.116 -1.131
41 H10 H H10 N N N 0 -8.3 0.336 -2.48
42 H11 H H11 N N N 0 -8.717 4.018 0.178
43 H12 H H12 N N N 0 -7.386 4.005 1.202
44 H13 H H13 N N N 0 -3.544 1.156 1.891
45 H14 H H14 N N N 0 -4.672 -1.867 1.748
46 H15 H H15 N N N 0 -5.181 -2.656 0.216
47 H16 H H16 N N N 0 -2.999 -3.611 -0.15
48 H17 H H17 N N N 0 -3.798 -4.49 1.96



V3A : Chemical Bonds

Total Number of Bonds: 50
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C2 N1 C N doub 1.32 N Y
2 C2 N3 C N sing 1.32 N Y
3 N1 C6 N C sing 1.33 N Y
4 N3 C4 N C doub 1.33 N Y
5 C6 N6 C N sing 1.38 N N
6 C6 C5 C C doub 1.41 N Y
7 C4 C5 C C sing 1.41 N Y
8 C4 N9 C N sing 1.37 N Y
9 C2' C1' C C sing 1.55 N N
10 C2' C3' C C sing 1.55 N N
11 C5 N7 C N sing 1.36 N Y
12 N9 C1' N C sing 1.47 N N
13 N9 C8 N C sing 1.36 N Y
14 C1' O4' C O sing 1.44 N N
15 O3' C3' O C sing 1.43 N N
16 C3' C4' C C sing 1.54 N N
17 O4' C4' O C sing 1.43 N N
18 N7 C8 N C doub 1.3 N Y
19 C4' C5' C C sing 1.53 N N
20 O2B PB O P doub 1.48 N N
21 C5' O5' C O sing 1.43 N N
22 O5' PA O P sing 1.61 N N
23 PB O3A P O sing 1.61 N N
24 PB O1B P O sing 1.61 N N
25 PB C3B P C sing 1.82 N N
26 F3B C3B F C sing 1.4 N N
27 O3A PA O P sing 1.61 N N
28 PA O2A P O doub 1.48 N N
29 PA O1A P O sing 1.61 N N
30 C3B PG C P sing 1.82 N N
31 PG O3G P O doub 1.48 N N
32 PG O1G P O sing 1.61 N N
33 PG O2G P O sing 1.61 N N
34 O1A H1 O H sing 0.97 N N
35 O1B H2 O H sing 0.97 N N
36 C3B H3 C H sing 1.09 N N
37 O1G H4 O H sing 0.97 N N
38 O2G H5 O H sing 0.97 N N
39 C5' H6 C H sing 1.09 N N
40 C5' H7 C H sing 1.09 N N
41 C4' H8 C H sing 1.09 N N
42 C1' H9 C H sing 1.09 N N
43 C2 H10 C H sing 1.08 N N
44 N6 H11 N H sing 0.97 N N
45 N6 H12 N H sing 0.97 N N
46 C8 H13 C H sing 1.08 N N
47 C2' H14 C H sing 1.09 N N
48 C2' H15 C H sing 1.09 N N
49 C3' H16 C H sing 1.09 N N
50 O3' H17 O H sing 0.97 N N



V3A : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
V3A 6cr7 Open in New Window Bound ligand 1 1