Chemical Components in the PDB

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VA5 : Summary

Code

VA5

One-letter code

X

Molecule name

9-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-D-threo-pentofuranosyl}-9H-purin-6-amine

Systematic names

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

Formula

C11 H16 Cl F N5 O11 P3

Formal charge

0

Molecular weight

541.644 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 P(=O)(O)(OP(O)(C(Cl)(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)[C](F)(Cl)[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)Cl)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@@](F)(Cl)[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@](F)(P(=O)(O)O)Cl)O)O)N

IUPAC InChI

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

MGXOAMBWOAGILL-FHZUQPTBSA-N
VA5

wwPDB Information

Atom count

48 (32 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



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
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 1.4 N Y
8 C4 N9 C N sing 1.37 N Y
9 C2' C3' C C sing 1.55 N N
10 C2' C1' C C sing 1.55 N N
11 C5 N7 C N sing 1.35 N Y
12 C3' O3' C O sing 1.43 N N
13 C3' C4' C C sing 1.54 N N
14 N9 C1' N C sing 1.46 N N
15 N9 C8 N C sing 1.36 N Y
16 C1' O4' C O sing 1.44 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 O3A PA O P sing 1.61 N N
27 F3B C3B F C sing 1.4 N N
28 PA O2A P O doub 1.48 N N
29 PA O1A P O sing 1.61 N N
30 C3B CL1 C CL sing 1.8 N N
31 C3B PG C P sing 1.82 N N
32 O3G PG O P doub 1.48 N N
33 PG O1G P O sing 1.61 N N
34 PG O2G P O sing 1.61 N N
35 O1A H1 O H sing 0.97 N N
36 O1B H2 O H sing 0.97 N N
37 O1G H3 O H sing 0.97 N N
38 O2G H4 O H sing 0.97 N N
39 C5' H5 C H sing 1.09 N N
40 C5' H6 C H sing 1.09 N N
41 C4' H7 C H sing 1.09 N N
42 C1' H8 C H sing 1.09 N N
43 C2 H9 C H sing 1.08 N N
44 N6 H10 N H sing 0.97 N N
45 N6 H11 N H sing 0.97 N N
46 C8 H12 C H sing 1.08 N N
47 C2' H13 C H sing 1.09 N N
48 C2' H14 C H sing 1.09 N N
49 C3' H15 C H sing 1.09 N N
50 O3' H16 O H sing 0.97 N N



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 Bound ligand 1 1