Chemical Components in the PDB

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9ZA : Summary

Code

9ZA

One-letter code

X

Molecule name

[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-~{N}-[(2~{S})-1-methoxy-1-oxidanylidene-propan-2-yl]phosphonamidic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 methyl (2S)-2-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]amino}propanoate (non-preferred name)
OpenEye OEToolkits 2.0.6 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-~{N}-[(2~{S})-1-methoxy-1-oxidanylidene-propan-2-yl]phosphonamidic acid

Formula

C14 H21 N6 O8 P

Formal charge

0

Molecular weight

432.326 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OP(=O)(OCC1C(O)C(O)C(O1)n3c2ncnc(c2nc3)N)NC(C(OC)=O)C
SMILES CACTVS 3.385 COC(=O)[CH](C)N[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
SMILES OpenEye OEToolkits 2.0.6 CC(C(=O)OC)NP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Canonical SMILES CACTVS 3.385 COC(=O)[C@H](C)N[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
Canonical SMILES OpenEye OEToolkits 2.0.6 C[C@@H](C(=O)OC)NP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O

IUPAC InChI

InChI=1S/C14H21N6O8P/c1-6(14(23)26-2)19-29(24,25)27-3-7-9(21)10(22)13(28-7)20-5-18-8-11(15)16-4-17-12(8)20/h4-7,9-10,13,21-22H,3H2,1-2H3,(H2,15,16,17)(H2,19,24,25)/t6-,7+,9+,10+,13+/m0/s1

IUPAC InChI key

KHSIAISBDZSYJB-WFMPWKQPSA-N
9ZA

wwPDB Information

Atom count

50 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-06-28

Last modified at

2017-10-13

Status

Released

Obsoleted

Not Assigned



9ZA : Atoms of Molecule

Total Number of Atoms: 50
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O3P O O1 N N N 0 3.471 -2.635 -0.892
2 P P P1 N N N 0 3.156 -1.69 0.373
3 O2P O O2 N N N 0 2.861 -2.53 1.555
4 O5' O O3 N N N 0 1.883 -0.761 0.044
5 C5' C C1 N N N 0 1.225 0.037 1.032
6 C4' C C2 R N N 0 0.062 0.791 0.386
7 C3' C C3 S N N 0 -0.61 1.727 1.416
8 O3' O O4 N N N 0 -0.132 3.065 1.263
9 C2' C C4 R N N 0 -2.114 1.646 1.071
10 O2' O O5 N N N 0 -2.612 2.933 0.698
11 C1' C C5 R N N 0 -2.173 0.672 -0.127
12 O4' O O6 N N N 0 -0.977 -0.131 -0.011
13 N9 N N1 N Y N 0 -3.366 -0.174 -0.038
14 C4 C C6 N Y N 0 -4.623 0.146 -0.484
15 C5 C C7 N Y N 0 -5.433 -0.963 -0.187
16 N7 N N2 N Y N 0 -4.644 -1.885 0.415
17 C8 C C8 N Y N 0 -3.429 -1.426 0.498
18 N3 N N3 N Y N 0 -5.166 1.2 -1.085
19 C2 C C9 N Y N 0 -6.444 1.21 -1.398
20 N1 N N4 N Y N 0 -7.245 0.192 -1.138
21 C6 C C10 N Y N 0 -6.793 -0.903 -0.537
22 N6 N N5 N N N 0 -7.64 -1.965 -0.269
23 N2 N N6 N N N 0 4.492 -0.718 0.693
24 C3 C C11 S N N 0 4.814 0.132 -0.461
25 C7 C C12 N N N 0 6.308 0.303 -0.557
26 C9 C C13 N N N 0 4.154 1.501 -0.286
27 O10 O O7 N N N 0 7.03 -0.229 0.252
28 O11 O O8 N N N 0 6.836 1.045 -1.543
29 C12 C C14 N N N 0 8.283 1.166 -1.574
30 H1 H H1 N N N 0 3.673 -2.151 -1.704
31 H2 H H2 N N N 0 0.846 -0.607 1.825
32 H3 H H3 N N N 0 1.934 0.751 1.451
33 H4 H H4 N N N 0 0.411 1.362 -0.474
34 H5 H H5 N N N 0 -0.429 1.371 2.43
35 H6 H H6 N N N 0 -0.522 3.694 1.885
36 H7 H H7 N N N 0 -2.679 1.249 1.914
37 H8 H H8 N N N 0 -2.543 3.598 1.395
38 H9 H H9 N N N 0 -2.168 1.224 -1.066
39 H10 H H10 N N N 0 -2.595 -1.956 0.934
40 H11 H H11 N N N 0 -6.853 2.082 -1.885
41 H12 H H12 N N N 0 -8.576 -1.914 -0.521
42 H13 H H13 N N N 0 -7.299 -2.759 0.17
43 H14 H H14 N N N 0 4.344 -0.161 1.522
44 H15 H H15 N N N 0 4.442 -0.337 -1.372
45 H16 H H16 N N N 0 4.525 1.97 0.625
46 H17 H H17 N N N 0 4.393 2.131 -1.143
47 H18 H H18 N N N 0 3.073 1.377 -0.217
48 H19 H H19 N N N 0 8.63 1.622 -0.646
49 H20 H H20 N N N 0 8.728 0.177 -1.682
50 H21 H H21 N N N 0 8.577 1.791 -2.417



9ZA : Chemical Bonds

Total Number of Bonds: 52
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N6 C6 N C sing 1.38 N N
2 C6 N1 C N doub 1.33 N Y
3 C6 C5 C C sing 1.41 N Y
4 N1 C2 N C sing 1.32 N Y
5 C5 N7 C N sing 1.35 N Y
6 C5 C4 C C doub 1.41 N Y
7 C2 N3 C N doub 1.32 N Y
8 N7 C8 N C doub 1.3 N Y
9 C4 N3 C N sing 1.33 N Y
10 C4 N9 C N sing 1.37 N Y
11 C8 N9 C N sing 1.36 N Y
12 N9 C1' N C sing 1.47 N N
13 C1' C2' C C sing 1.55 N N
14 C1' O4' C O sing 1.45 N N
15 O2' C2' O C sing 1.43 N N
16 C2' C3' C C sing 1.55 N N
17 O4' C4' O C sing 1.44 N N
18 C3' C4' C C sing 1.55 N N
19 C3' O3' C O sing 1.43 N N
20 C4' C5' C C sing 1.53 N N
21 C5' O5' C O sing 1.43 N N
22 O5' P O P sing 1.61 N N
23 O10 C7 O C doub 1.21 N N
24 O2P P O P doub 1.48 N N
25 N2 P N P sing 1.68 N N
26 N2 C3 N C sing 1.47 N N
27 P O3P P O sing 1.61 N N
28 C7 C3 C C sing 1.51 N N
29 C7 O11 C O sing 1.34 N N
30 C9 C3 C C sing 1.53 N N
31 C12 O11 C O sing 1.45 N N
32 O3P H1 O H sing 0.97 N N
33 C5' H2 C H sing 1.09 N N
34 C5' H3 C H sing 1.09 N N
35 C4' H4 C H sing 1.09 N N
36 C3' H5 C H sing 1.09 N N
37 O3' H6 O H sing 0.97 N N
38 C2' H7 C H sing 1.09 N N
39 O2' H8 O H sing 0.97 N N
40 C1' H9 C H sing 1.09 N N
41 C8 H10 C H sing 1.08 N N
42 C2 H11 C H sing 1.08 N N
43 N6 H12 N H sing 0.97 N N
44 N6 H13 N H sing 0.97 N N
45 N2 H14 N H sing 1.01 N N
46 C3 H15 C H sing 1.09 N N
47 C9 H16 C H sing 1.09 N N
48 C9 H17 C H sing 1.09 N N
49 C9 H18 C H sing 1.09 N N
50 C12 H19 C H sing 1.09 N N
51 C12 H20 C H sing 1.09 N N
52 C12 H21 C H sing 1.09 N N



9ZA : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
9ZA 5wa8 Open in New Window Bound ligand 1 1