Chemical Components in the PDB

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RP1 : Summary

Code

RP1

One-letter code

X

Molecule name

6-(6-AMINO-PURIN-9-YL)-2-THIOXO-TETRAHYDRO-2-FURO[3,2-D][1,3,2]DIOXAPHOSPHININE-2,7-DIOL

Systematic names

ProgramVersionName
ACDLabs 10.04 (2R,4aR,6R,7R,7aS)-6-(6-amino-9H-purin-9-yl)tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol 2-sulfide
OpenEye OEToolkits 1.5.0 (1R,4R,6S,7R,8R)-8-(6-aminopurin-9-yl)-4-hydroxy-4-sulfanylidene-3,5,9-trioxa-4$l^{5}-phosphabicyclo[4.3.0]nonan-7-ol

Formula

C10 H12 N5 O5 P S

Formal charge

0

Molecular weight

345.272 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 S=P3(OCC4OC(n1c2ncnc(N)c2nc1)C(O)C4O3)O
SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=S)O[CH]4[CH]3O
SMILES OpenEye OEToolkits 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=S)(O4)O)O)N
Canonical SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P@@](O)(=S)O[C@H]4[C@H]3O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=S)(O4)O)O)N

IUPAC InChI

InChI=1S/C10H12N5O5PS/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7-4(19-10)1-18-21(17,22)20-7/h2-4,6-7,10,16H,1H2,(H,17,22)(H2,11,12,13)/t4-,6-,7-,10-,21-/m1/s1

IUPAC InChI key

SMPNJFHAPJOHPP-PUHOFUEYSA-N
RP1

wwPDB Information

Atom count

34 (22 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2002-12-13

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



RP1 : Atoms of Molecule

Total Number of Atoms: 34
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P R N N 0 -3.849 0.11 0.375
2 S1P S S1P N N N 0 -5.446 -0.826 0.593
3 O2P O O2P N N N 0 -3.706 1.195 1.556
4 O5' O O5* N N N 0 -3.871 0.869 -1.041
5 C5' C C5* N N N 0 -2.597 1.497 -1.242
6 C4' C C4* R N N 0 -1.537 0.411 -1.211
7 C2' C C2* R N N 0 -0.13 -0.926 0.179
8 O4' O O4* N N N 0 -0.2 0.842 -1.464
9 C3' C C3* S N N 0 -1.455 -0.145 0.235
10 O3' O O3* N N N 0 -2.612 -0.927 0.453
11 O2' O O2* N N N 0 -0.367 -2.298 -0.143
12 C1' C C1* R N N 0 0.652 -0.211 -0.951
13 N9 N N9 N Y N 0 1.888 0.365 -0.415
14 C8 C C8 N Y N 0 2.059 1.645 0.022
15 N7 N N7 N Y N 0 3.282 1.815 0.431
16 C5 C C5 N Y N 0 3.971 0.657 0.289
17 C6 C C6 N Y N 0 5.292 0.255 0.547
18 N6 N N6 N N N 0 6.21 1.142 1.083
19 N1 N N1 N Y N 0 5.639 -0.997 0.269
20 C2 C C2 N Y N 0 4.77 -1.85 -0.243
21 N3 N N3 N Y N 0 3.524 -1.516 -0.506
22 C4 C C4 N Y N 0 3.086 -0.286 -0.262
23 HOP2 H 2HOP N N N 0 -4.472 1.781 1.491
24 H5'1 H 1H5* N N N 0 -2.41 2.218 -0.446
25 H5'2 H 2H5* N N N 0 -2.582 2.0 -2.209
26 H4' H H4* N N N 0 -1.806 -0.388 -1.901
27 H3' H H3* N N N 0 -1.402 0.674 0.953
28 H2' H H2* N N N 0 0.407 -0.841 1.124
29 HO2' H *HO2 N N N 0 0.496 -2.733 -0.164
30 H1' H H1* N N N 0 0.886 -0.919 -1.746
31 H8 H H8 N N N 0 1.292 2.405 0.027
32 HN61 H 1HN6 N N N 0 7.118 0.851 1.26
33 HN62 H 2HN6 N N N 0 5.946 2.055 1.277
34 H2 H H2 N N N 0 5.094 -2.858 -0.453



RP1 : Chemical Bonds

Total Number of Bonds: 37
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P S1P P S doub 1.86 N N
2 P O2P P O sing 1.61 N N
3 P O5' P O sing 1.61 N N
4 P O3' P O sing 1.62 N N
5 O2P HOP2 O H sing 0.97 N N
6 O5' C5' O C sing 1.43 N N
7 C5' C4' C C sing 1.52 N N
8 C5' H5'1 C H sing 1.09 N N
9 C5' H5'2 C H sing 1.09 N N
10 C4' O4' C O sing 1.43 N N
11 C4' C3' C C sing 1.55 N N
12 C4' H4' C H sing 1.09 N N
13 O4' C1' O C sing 1.45 N N
14 C3' O3' C O sing 1.41 N N
15 C3' C2' C C sing 1.54 N N
16 C3' H3' C H sing 1.09 N N
17 C2' O2' C O sing 1.43 N N
18 C2' C1' C C sing 1.55 N N
19 C2' H2' C H sing 1.09 N N
20 O2' HO2' O H sing 0.97 N N
21 C1' N9 C N sing 1.47 N N
22 C1' H1' C H sing 1.09 N N
23 N9 C8 N C sing 1.36 N Y
24 N9 C4 N C sing 1.37 N Y
25 C8 N7 C N doub 1.3 N Y
26 C8 H8 C H sing 1.08 N N
27 N7 C5 N C sing 1.35 N Y
28 C5 C6 C C doub 1.4 N Y
29 C5 C4 C C sing 1.41 N Y
30 C6 N6 C N sing 1.38 N N
31 C6 N1 C N sing 1.33 N Y
32 N6 HN61 N H sing 0.97 N N
33 N6 HN62 N H sing 0.97 N N
34 N1 C2 N C doub 1.32 N Y
35 C2 N3 C N sing 1.32 N Y
36 C2 H2 C H sing 1.08 N N
37 N3 C4 N C doub 1.33 N Y



RP1 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
RP1 1ne4 Open in New Window Bound ligand 2 1