Chemical Components in the PDB

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B4P : Summary

Code

B4P

One-letter code

X

Molecule name

BIS(ADENOSINE)-5'-TETRAPHOSPHATE

Systematic names

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

Formula

C20 H28 N10 O19 P4

Formal charge

0

Molecular weight

836.387 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=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)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)N
Canonical SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P@](O)(=O)O[P@](O)(=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)(O)O[P@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)N

IUPAC InChI

InChI=1S/C20H28N10O19P4/c21-15-9-17(25-3-23-15)29(5-27-9)19-13(33)11(31)7(45-19)1-43-50(35,36)47-52(39,40)49-53(41,42)48-51(37,38)44-2-8-12(32)14(34)20(46-8)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-34H,1-2H2,(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1

IUPAC InChI key

YOAHKNVSNCMZGQ-XPWFQUROSA-N
B4P

wwPDB Information

Atom count

81 (53 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2005-08-25

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



B4P : Atoms of Molecule

Total Number of Atoms: 81
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1E C AC1* R N N 0 8.933 -0.962 -0.36
2 C1F C BC1* R N N 0 -8.975 0.987 -0.375
3 C2A C AC2 N Y N 0 12.901 0.864 -1.391
4 C2B C BC2 N Y N 0 -12.872 -1.131 -1.06
5 C2E C AC2* R N N 0 9.306 -1.843 0.853
6 C2F C BC2* R N N 0 -9.178 1.698 0.987
7 C3E C AC3* S N N 0 8.044 -2.705 1.092
8 C3F C BC3* S N N 0 -8.156 2.862 0.902
9 C4A C AC4 N Y N 0 10.751 0.784 -0.582
10 C4B C BC4 N Y N 0 -10.646 -0.907 -0.535
11 C4E C AC4* R N N 0 7.061 -2.245 -0.0070
12 C4F C BC4* R N N 0 -7.15 2.398 -0.171
13 C5A C AC5 N Y N 0 10.842 2.143 -0.237
14 C5B C BC5 N Y N 0 -10.564 -2.297 -0.34
15 C5E C AC5* N N N 0 5.629 -2.224 0.531
16 C5F C BC5* N N N 0 -5.742 2.343 0.426
17 C6A C AC6 N Y N 0 12.04 2.82 -0.52
18 C6B C BC6 N Y N 0 -11.727 -3.063 -0.527
19 C8A C AC8 N Y N 0 8.864 1.462 0.335
20 C8B C BC8 N Y N 0 -8.593 -1.473 0.038
21 H1E H AH1* N N N 0 9.288 -1.418 -1.284
22 H1F H BH1* N N N 0 -9.523 1.503 -1.163
23 H2A H AH2 N N N 0 13.732 0.352 -1.853
24 H2B H BH2 N N N 0 -13.803 -0.665 -1.35
25 H2E H AH2* N N N 0 9.515 -1.223 1.724
26 H2F H BH2* N N N 0 -8.939 1.029 1.814
27 H3E H AH3* N N N 0 7.629 -2.512 2.081
28 H3F H BH3* N N N 0 -7.654 3.0 1.86
29 H4E H AH4* N N N 0 7.13 -2.899 -0.876
30 H4F H BH4* N N N 0 -7.168 3.085 -1.017
31 H51A H AH51 N N N 0 5.361 -3.217 0.89
32 H51B H BH51 N N N 0 -5.707 1.581 1.204
33 H52A H AH52 N N N 0 5.559 -1.509 1.351
34 H52B H BH52 N N N 0 -5.491 3.313 0.855
35 H61A H AH61 N N N 0 13.02 4.616 -0.403
36 H61B H BH61 N N N 0 -10.885 -4.878 -0.083
37 H62A H AH62 N N N 0 11.455 4.645 0.205
38 H62B H BH62 N N N 0 -12.517 -4.952 -0.476
39 H8A H AH8 N N N 0 7.857 1.461 0.725
40 H8B H BH8 N N N 0 -7.545 -1.406 0.287
41 HO2A H AHO2 N N N 0 10.574 -3.24 1.32
42 HO2B H BHO2 N N N 0 -10.571 2.627 1.972
43 HO3A H AHO3 N N N 0 8.964 -4.323 1.651
44 HO3B H BHO3 N N N 0 -9.461 4.273 1.179
45 HOA2 H 2HOA N N N 0 2.876 -3.87 -0.266
46 HOB2 H 2HOB N N N 0 -0.188 -2.58 -0.482
47 HOD2 H 2HOD N N N 0 -2.961 4.031 -0.154
48 HOG2 H 2HOG N N N 0 0.112 2.752 -0.316
49 N1A N AN1 N Y N 0 13.032 2.143 -1.09
50 N1B N BN1 N Y N 0 -12.845 -2.44 -0.883
51 N3A N AN3 N Y N 0 11.796 0.19 -1.15
52 N3B N BN3 N Y N 0 -11.808 -0.374 -0.897
53 N6A N AN6 N N N 0 12.187 4.161 -0.207
54 N6B N BN6 N N N 0 -11.708 -4.434 -0.344
55 N7A N AN7 N Y N 0 9.656 2.495 0.314
56 N7B N BN7 N Y N 0 -9.285 -2.575 0.011
57 N9A N AN9 N Y N 0 9.495 0.382 -0.206
58 N9B N BN9 N Y N 0 -9.388 -0.417 -0.295
59 O1A O O1A N N N 0 3.228 -0.965 1.315
60 O1B O O1B N N N 0 1.312 -0.024 1.028
61 O1D O O1D N N N 0 -3.376 1.037 1.235
62 O1G O O1G N N N 0 -1.448 0.112 0.973
63 O2A O O2A N N N 0 2.848 -3.337 0.54
64 O2B O O2B N N N 0 0.062 -2.098 0.318
65 O2D O O2D N N N 0 -2.966 3.451 0.619
66 O2E O AO2* N N N 0 10.429 -2.673 0.55
67 O2F O BO2* N N N 0 -10.511 2.199 1.107
68 O2G O O2G N N N 0 -0.171 2.224 0.443
69 O3A O O3A N N N 0 2.204 -1.283 -0.97
70 O3B O O3B N N N 0 -0.023 0.107 -1.11
71 O3E O AO3* N N N 0 8.349 -4.093 0.941
72 O3F O BO3* N N N 0 -8.805 4.069 0.499
73 O3G O O3G N N N 0 -2.256 1.49 -0.981
74 O4E O AO4* N N N 0 7.489 -0.908 -0.349
75 O4F O BO4* N N N 0 -7.552 1.086 -0.598
76 O5E O AO5* N N N 0 4.733 -1.837 -0.514
77 O5F O BO5* N N N 0 -4.803 2.019 -0.601
78 PA P PA S N N 0 3.253 -1.837 0.119
79 PB P PB S N N 0 0.898 -0.807 -0.157
80 PD P PD S N N 0 -3.351 1.979 0.093
81 PG P PG S N N 0 -0.985 0.965 -0.144



B4P : Chemical Bonds

Total Number of Bonds: 86
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 O3A P O sing 1.61 N N
4 PA O5E P O sing 1.61 N N
5 O2A HOA2 O H sing 0.97 N N
6 O3A PB O P sing 1.61 N N
7 PB O1B P O doub 1.48 N N
8 PB O2B P O sing 1.61 N N
9 PB O3B P O sing 1.61 N N
10 O2B HOB2 O H sing 0.97 N N
11 O3B PG O P sing 1.61 N N
12 PG O1G P O doub 1.48 N N
13 PG O2G P O sing 1.61 N N
14 PG O3G P O sing 1.61 N N
15 O2G HOG2 O H sing 0.97 N N
16 O3G PD O P sing 1.61 N N
17 PD O1D P O doub 1.48 N N
18 PD O2D P O sing 1.61 N N
19 PD O5F P O sing 1.61 N N
20 O2D HOD2 O H sing 0.97 N N
21 O5E C5E O C sing 1.43 N N
22 C5E C4E C C sing 1.53 N N
23 C5E H51A C H sing 1.09 N N
24 C5E H52A C H sing 1.09 N N
25 C4E O4E C O sing 1.44 N N
26 C4E C3E C C sing 1.54 N N
27 C4E H4E C H sing 1.09 N N
28 O4E C1E O C sing 1.45 N N
29 C3E O3E C O sing 1.43 N N
30 C3E C2E C C sing 1.55 N N
31 C3E H3E C H sing 1.09 N N
32 O3E HO3A O H sing 0.97 N N
33 C2E O2E C O sing 1.43 N N
34 C2E C1E C C sing 1.54 N N
35 C2E H2E C H sing 1.09 N N
36 O2E HO2A O H sing 0.97 N N
37 C1E N9A C N sing 1.46 N N
38 C1E H1E C H sing 1.09 N N
39 N9A C8A N C sing 1.36 N Y
40 N9A C4A N C sing 1.37 N Y
41 C8A N7A C N doub 1.3 N Y
42 C8A H8A C H sing 1.08 N N
43 N7A C5A N C sing 1.35 N Y
44 C5A C6A C C sing 1.4 N Y
45 C5A C4A C C doub 1.41 N Y
46 C6A N6A C N sing 1.38 N N
47 C6A N1A C N doub 1.33 N Y
48 N6A H61A N H sing 0.97 N N
49 N6A H62A N H sing 0.97 N N
50 N1A C2A N C sing 1.32 N Y
51 C2A N3A C N doub 1.32 N Y
52 C2A H2A C H sing 1.08 N N
53 N3A C4A N C sing 1.33 N Y
54 O5F C5F O C sing 1.43 N N
55 C5F C4F C C sing 1.53 N N
56 C5F H51B C H sing 1.09 N N
57 C5F H52B C H sing 1.09 N N
58 C4F O4F C O sing 1.44 N N
59 C4F C3F C C sing 1.54 N N
60 C4F H4F C H sing 1.09 N N
61 O4F C1F O C sing 1.44 N N
62 C3F O3F C O sing 1.43 N N
63 C3F C2F C C sing 1.55 N N
64 C3F H3F C H sing 1.09 N N
65 O3F HO3B O H sing 0.97 N N
66 C2F O2F C O sing 1.43 N N
67 C2F C1F C C sing 1.55 N N
68 C2F H2F C H sing 1.09 N N
69 O2F HO2B O H sing 0.97 N N
70 C1F N9B C N sing 1.47 N N
71 C1F H1F C H sing 1.09 N N
72 N9B C8B N C sing 1.36 N Y
73 N9B C4B N C sing 1.37 N Y
74 C8B N7B C N doub 1.3 N Y
75 C8B H8B C H sing 1.08 N N
76 N7B C5B N C sing 1.36 N Y
77 C5B C6B C C sing 1.41 N Y
78 C5B C4B C C doub 1.41 N Y
79 C6B N6B C N sing 1.38 N N
80 C6B N1B C N doub 1.33 N Y
81 N6B H61B N H sing 0.97 N N
82 N6B H62B N H sing 0.97 N N
83 N1B C2B N C sing 1.32 N Y
84 C2B N3B C N doub 1.32 N Y
85 C2B H2B C H sing 1.08 N N
86 N3B C4B N C sing 1.33 N Y



B4P : Used in PDB Entries

Total Number of PDB Entries: 20
Ligand Code PDB Entry ID Type Total Distinct
B4P 2c05 Open in New Window Bound ligand 1 1
B4P 2c95 Open in New Window Bound ligand 2 1
B4P 2c9y Open in New Window Bound ligand 1 1
B4P 2e1z Open in New Window Bound ligand 1 1
B4P 2e20 Open in New Window Bound ligand 1 1
B4P 2xjc Open in New Window Bound ligand 1 1
B4P 2zt5 Open in New Window Bound ligand 1 1
B4P 2zxf Open in New Window Bound ligand 1 1
B4P 3a74 Open in New Window Bound ligand 4 1
B4P 3bho Open in New Window Bound ligand 1 1
B4P 3i7v Open in New Window Bound ligand 1 1
B4P 3l2b Open in New Window Bound ligand 1 1
B4P 3loo Open in New Window Bound ligand 3 1
B4P 3rqx Open in New Window Bound ligand 3 1
B4P 3rsf Open in New Window Bound ligand 1 1
B4P 4i5v Open in New Window Bound ligand 2 1
B4P 5yzx Open in New Window Bound ligand 3 1
B4P 6f2y Open in New Window Bound ligand 2 1
B4P 6j64 Open in New Window Bound ligand 1 1
B4P 6j65 Open in New Window Bound ligand 1 1