Chemical Components in the PDB

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IB2 : Summary

Code

IB2

One-letter code

X

Molecule name

P1-P2-METHYLENE-P3-THIO-DIADENOSINE TRIPHOSPHATE

Synonyms

ADO-P-CH2-P-PS-ADO

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-hydroxy-phosphoryl]methyl]phosphinic acid

Formula

C21 H29 N10 O14 P3 S

Formal charge

0

Molecular weight

770.5 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](S)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)S)O)O)O)N
Canonical SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)C[P@@](O)(=O)O[P@@](S)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)[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)(C[P@](=O)(O)O[P@@](=O)(OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)S)O)O)O)N

IUPAC InChI

InChI=1S/C21H29N10O14P3S/c22-16-10-18(26-3-24-16)30(5-28-10)20-14(34)12(32)8(43-20)1-41-46(36,37)7-47(38,39)45-48(40,49)42-2-9-13(33)15(35)21(44-9)31-6-29-11-17(23)25-4-27-19(11)31/h3-6,8-9,12-15,20-21,32-35H,1-2,7H2,(H,36,37)(H,38,39)(H,40,49)(H2,22,24,26)(H2,23,25,27)/t8-,9-,12-,13-,14-,15-,20-,21-,48-/m1/s1

IUPAC InChI key

UJCWOSLCGXVJOD-LCHUORCTSA-N
IB2

wwPDB Information

Atom count

78 (49 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

2021-03-01

Status

Released

Obsoleted

Not Assigned



IB2 : Atoms of Molecule

Total Number of Atoms: 78
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 PA P PA S N N 0 -0.622 1.325 2.707
2 O1A O O1A N N N 0 -1.719 2.235 2.309
3 O2A O O2A N N N 0 0.688 2.189 3.062
4 C3A C C3A N N N 0 -0.247 0.187 1.334
5 PB P PB S N N 0 0.261 1.148 -0.129
6 O1B O O1B N N N 0 1.466 1.942 0.196
7 O2B O O2B N N N 0 -0.932 2.137 -0.563
8 O3B O O3B N N N 0 0.592 0.143 -1.342
9 PG P PG R N N 0 1.032 1.054 -2.594
10 O1G O O1G N N N 0 2.226 1.85 -2.23
11 S2G S S2G N N N 0 -0.556 2.359 -3.111
12 O5D O O5* N N N 0 -1.071 0.477 4.0
13 C5D C C5* N N N 0 -1.35 1.42 5.037
14 C4D C C4* R N N 0 -1.785 0.675 6.3
15 O4D O O4* N N N 0 -0.726 -0.19 6.763
16 C3D C C3* S N N 0 -2.018 1.668 7.46
17 O3D O O3* N N N 0 -3.409 1.968 7.591
18 C2D C C2* R N N 0 -1.506 0.915 8.71
19 O2D O O2* N N N 0 -2.564 0.729 9.651
20 C1D C C1* R N N 0 -1.021 -0.442 8.154
21 O5' O O5' N N N 0 1.38 0.109 -3.85
22 C5' C C5' N N N 0 1.761 0.971 -4.924
23 C4' C C4' R N N 0 2.106 0.132 -6.155
24 O4' O O4' N N N 0 0.953 -0.614 -6.577
25 C3' C C3' S N N 0 2.511 1.054 -7.322
26 O3' O O3' N N N 0 3.846 0.774 -7.748
27 C2' C C2' R N N 0 1.499 0.707 -8.444
28 O2' O O2' N N N 0 2.147 0.657 -9.717
29 C1' C C1' R N N 0 1.01 -0.7 -8.017
30 N9 N N9 N Y N 0 -0.317 -0.978 -8.571
31 C8 C C8 N Y N 0 -1.512 -0.623 -8.019
32 N7 N N7 N Y N 0 -2.489 -1.029 -8.775
33 C5 C C5 N Y N 0 -1.986 -1.669 -9.858
34 C6 C C6 N Y N 0 -2.546 -2.299 -10.982
35 N6 N N6 N N N 0 -3.918 -2.354 -11.153
36 N1 N N1 N Y N 0 -1.726 -2.841 -11.878
37 C2 C C2 N Y N 0 -0.416 -2.792 -11.723
38 N3 N N3 N Y N 0 0.152 -2.213 -10.687
39 C4 C C4 N Y N 0 -0.586 -1.639 -9.743
40 N9A N AN9 N Y N 0 0.184 -0.881 8.86
41 C8A C AC8 N Y N 0 1.47 -0.574 8.527
42 N7A N AN7 N Y N 0 2.292 -1.13 9.369
43 C5A C AC5 N Y N 0 1.588 -1.823 10.296
44 C6A C AC6 N Y N 0 1.927 -2.608 11.411
45 N6A N AN6 N N N 0 3.251 -2.794 11.77
46 N1A N AN1 N Y N 0 0.947 -3.164 12.115
47 C2A C AC2 N Y N 0 -0.318 -2.993 11.78
48 N3A N AN3 N Y N 0 -0.682 -2.271 10.741
49 C4A C AC4 N Y N 0 0.227 -1.676 9.977
50 HOA2 H 2HOA N N N 0 1.377 1.56 3.316
51 H3A1 H 1H3A N N N 0 0.56 -0.482 1.627
52 H3A2 H 2H3A N N N 0 -1.135 -0.397 1.094
53 HOB2 H 2HOB N N N 0 -1.696 1.581 -0.766
54 HSG2 H 2HSG N N N 0 -1.513 1.459 -3.399
55 H5'1 H 1H5* N N N 0 -2.15 2.087 4.715
56 H5'2 H 2H5* N N N 0 -0.454 2.002 5.249
57 H4D H H4* N N N 0 -2.69 0.098 6.107
58 H3D H H3* N N N 0 -1.445 2.582 7.301
59 HO3' H *HO3 N N N 0 -3.493 2.59 8.326
60 H2D H H2* N N N 0 -0.678 1.455 9.169
61 HO2' H *HO2 N N N 0 -2.863 1.61 9.914
62 H1D H H1* N N N 0 -1.807 -1.192 8.246
63 H51X H 1H5' N N N 0 0.935 1.642 -5.161
64 H52X H 2H5' N N N 0 2.631 1.557 -4.628
65 H4' H H4' N N N 0 2.924 -0.55 -5.921
66 H3' H H3' N N N 0 2.416 2.1 -7.031
67 HO3X H 'HO3 N N N 0 4.019 1.338 -8.515
68 H2' H H2' N N N 0 0.673 1.418 -8.458
69 HO2X H 'HO2 N N N 0 2.426 1.559 -9.924
70 H1' H H1' N N N 0 1.722 -1.464 -8.328
71 H8 H H8 N N N 0 -1.629 -0.084 -7.09
72 HN61 H 1HN6 N N N 0 -4.292 -2.793 -11.933
73 HN62 H 2HN6 N N N 0 -4.505 -1.955 -10.492
74 H2 H H2 N N N 0 0.212 -3.245 -12.475
75 H8A H AH8 N N N 0 1.763 0.039 7.689
76 HNA1 H 1HNA N N N 0 3.472 -3.335 12.544
77 HNA2 H 2HNA N N N 0 3.957 -2.386 11.245
78 H2A H AH2 N N N 0 -1.083 -3.463 12.38



IB2 : Chemical Bonds

Total Number of Bonds: 83
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 PA O1A P O doub 1.48 N N
2 PA O2A P O sing 1.61 N N
3 PA C3A P C sing 1.82 N N
4 PA O5D P O sing 1.61 N N
5 O2A HOA2 O H sing 0.97 N N
6 C3A PB C P sing 1.82 N N
7 C3A H3A1 C H sing 1.09 N N
8 C3A H3A2 C H sing 1.09 N N
9 PB O1B P O doub 1.48 N N
10 PB O2B P O sing 1.61 N N
11 PB O3B P O sing 1.61 N N
12 O2B HOB2 O H sing 0.97 N N
13 O3B PG O P sing 1.61 N N
14 PG O1G P O doub 1.48 N N
15 PG S2G P S sing 2.12 N N
16 PG O5' P O sing 1.61 N N
17 S2G HSG2 S H sing 1.34 N N
18 O5D C5D O C sing 1.43 N N
19 C5D C4D C C sing 1.53 N N
20 C5D H5'1 C H sing 1.09 N N
21 C5D H5'2 C H sing 1.09 N N
22 C4D O4D C O sing 1.44 N N
23 C4D C3D C C sing 1.54 N N
24 C4D H4D C H sing 1.09 N N
25 O4D C1D O C sing 1.44 N N
26 C3D O3D C O sing 1.43 N N
27 C3D C2D C C sing 1.55 N N
28 C3D H3D C H sing 1.09 N N
29 O3D HO3' O H sing 0.97 N N
30 C2D O2D C O sing 1.43 N N
31 C2D C1D C C sing 1.54 N N
32 C2D H2D C H sing 1.09 N N
33 O2D HO2' O H sing 0.97 N N
34 C1D N9A C N sing 1.46 N N
35 C1D H1D C H sing 1.09 N N
36 O5' C5' O C sing 1.43 N N
37 C5' C4' C C sing 1.53 N N
38 C5' H51X C H sing 1.09 N N
39 C5' H52X C H sing 1.09 N N
40 C4' O4' C O sing 1.44 N N
41 C4' C3' C C sing 1.54 N N
42 C4' H4' C H sing 1.09 N N
43 O4' C1' O C sing 1.44 N N
44 C3' O3' C O sing 1.43 N N
45 C3' C2' C C sing 1.55 N N
46 C3' H3' C H sing 1.09 N N
47 O3' HO3X O H sing 0.97 N N
48 C2' O2' C O sing 1.43 N N
49 C2' C1' C C sing 1.55 N N
50 C2' H2' C H sing 1.09 N N
51 O2' HO2X O H sing 0.97 N N
52 C1' N9 C N sing 1.46 N N
53 C1' H1' C H sing 1.09 N N
54 N9 C8 N C sing 1.36 N Y
55 N9 C4 N C sing 1.37 N Y
56 C8 N7 C N doub 1.3 N Y
57 C8 H8 C H sing 1.08 N N
58 N7 C5 N C sing 1.35 N Y
59 C5 C6 C C sing 1.4 N Y
60 C5 C4 C C doub 1.41 N Y
61 C6 N6 C N sing 1.38 N N
62 C6 N1 C N doub 1.33 N Y
63 N6 HN61 N H sing 0.97 N N
64 N6 HN62 N H sing 0.97 N N
65 N1 C2 N C sing 1.32 N Y
66 C2 N3 C N doub 1.32 N Y
67 C2 H2 C H sing 1.08 N N
68 N3 C4 N C sing 1.33 N Y
69 N9A C8A N C sing 1.36 N Y
70 N9A C4A N C sing 1.37 N Y
71 C8A N7A C N doub 1.3 N Y
72 C8A H8A C H sing 1.08 N N
73 N7A C5A N C sing 1.35 N Y
74 C5A C6A C C sing 1.41 N Y
75 C5A C4A C C doub 1.41 N Y
76 C6A N6A C N sing 1.38 N N
77 C6A N1A C N doub 1.33 N Y
78 N6A HNA1 N H sing 0.97 N N
79 N6A HNA2 N H sing 0.97 N N
80 N1A C2A N C sing 1.32 N Y
81 C2A N3A C N doub 1.32 N Y
82 C2A H2A C H sing 1.08 N N
83 N3A C4A N C sing 1.33 N Y



IB2 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
IB2 1fhi Open in New Window Bound ligand 1 1
IB2 2fhi Open in New Window Bound ligand 1 1