Chemical Components in the PDB

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D3U : Summary

Code

D3U

One-letter code

X

Molecule name

2-PCPA derivative

Systematic names

Not Assigned

Formula

C36 H41 N9 O15 P2

Formal charge

0

Molecular weight

901.71 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Cc1cc2N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)C6=NC(=O)NC(=O)[C]67[CH](C=CN7c2cc1C)c8ccccc8
SMILES OpenEye OEToolkits 2.0.7 Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C34N2C=CC4c5ccccc5)CC(C(C(COP(=O)(O)OP(=O)(O)OCC6C(C(C(O6)n7cnc8c7ncnc8N)O)O)O)O)O
Canonical SMILES CACTVS 3.385 Cc1cc2N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)C6=NC(=O)NC(=O)[C@]67[C@@H](C=CN7c2cc1C)c8ccccc8
Canonical SMILES OpenEye OEToolkits 2.0.7 Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)[C@@]34N2C=C[C@H]4c5ccccc5)C[C@@H]([C@@H]([C@@H](COP(=O)(O)OP(=O)(O)OC[C@@H]6[C@H]([C@H]([C@@H](O6)n7cnc8c7ncnc8N)O)O)O)O)O

IUPAC InChI

InChI=1S/C36H41N9O15P2/c1-17-10-21-22(11-18(17)2)45-9-8-20(19-6-4-3-5-7-19)36(45)33(41-35(52)42-34(36)51)43(21)12-23(46)27(48)24(47)13-57-61(53,54)60-62(55,56)58-14-25-28(49)29(50)32(59-25)44-16-40-26-30(37)38-15-39-31(26)44/h3-11,15-16,20,23-25,27-29,32,46-50H,12-14H2,1-2H3,(H,53,54)(H,55,56)(H2,37,38,39)(H,42,51,52)/t20-,23-,24+,25+,27-,28+,29+,32+,36-/m0/s1

IUPAC InChI key

LTYXJNFFNLDHFB-VXYXFEBYSA-N
D3U

wwPDB Information

Atom count

103 (62 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-06-20

Last modified at

2020-05-15

Status

Released

Obsoleted

Not Assigned



D3U : Atoms of Molecule

Total Number of Atoms: 103
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N Y N 0 10.28 2.46 -0.589
2 C5 C C2 N Y N 0 10.315 3.277 0.553
3 C6 C C3 N Y N 0 11.129 4.423 0.525
4 C8 C C4 N Y N 0 8.967 1.632 0.977
5 N1 N N1 N Y N 0 11.826 4.677 -0.578
6 N3 N N2 N Y N 0 11.012 2.796 -1.646
7 OAL O O1 N N N 0 -7.961 3.793 -2.372
8 CAK C C5 N N N 0 -7.192 3.4 -1.521
9 NAM N N3 N N N 0 -5.996 4.003 -1.321
10 CAN C C6 N N N 0 -5.12 3.491 -0.436
11 OAO O O2 N N N 0 -4.228 4.201 -0.01
12 NAP N N4 N N N 0 -5.201 2.222 -0.008
13 CAQ C C7 N N N 0 -6.291 1.522 -0.214
14 CAJ C C8 S N N 0 -7.532 2.234 -0.647
15 CCB C C9 S N N 0 -8.383 2.747 0.545
16 CCE C C10 N Y N 0 -8.375 1.766 1.689
17 CCF C C11 N Y N 0 -7.889 2.149 2.925
18 CCG C C12 N Y N 0 -7.882 1.249 3.974
19 CCH C C13 N Y N 0 -8.362 -0.034 3.787
20 CCI C C14 N Y N 0 -8.849 -0.417 2.552
21 CCJ C C15 N Y N 0 -8.86 0.485 1.504
22 CCD C C16 N N N 0 -9.754 2.806 -0.132
23 CCC C C17 N N N 0 -9.732 1.953 -1.157
24 NAI N N5 N N N 0 -8.509 1.301 -1.219
25 CAH C C18 N Y N 0 -8.225 -0.019 -1.558
26 CAG C C19 N Y N 0 -9.007 -0.748 -2.432
27 CAE C C20 N Y N 0 -8.687 -2.067 -2.703
28 CAF C C21 N N N 0 -9.535 -2.865 -3.659
29 CAC C C22 N Y N 0 -7.59 -2.653 -2.098
30 CAD C C23 N N N 0 -7.259 -4.095 -2.386
31 CAB C C24 N Y N 0 -6.795 -1.926 -1.232
32 CAA C C25 N Y N 0 -7.096 -0.6 -0.965
33 NAR N N6 N N N 0 -6.254 0.173 -0.16
34 CAS C C26 N N N 0 -5.332 -0.489 0.767
35 CAT C C27 S N N 0 -3.952 -0.605 0.118
36 OAU O O3 N N N 0 -4.027 -1.485 -1.006
37 CAV C C28 S N N 0 -2.955 -1.161 1.136
38 OAW O O4 N N N 0 -2.88 -0.281 2.259
39 CAX C C29 R N N 0 -1.574 -1.277 0.486
40 OAY O O5 N N N 0 -1.649 -2.157 -0.637
41 CAZ C C30 N N N 0 -0.577 -1.833 1.505
42 OBA O O6 N N N 0 0.734 -1.833 0.936
43 PBB P P1 N N N 0 2.035 -2.353 1.73
44 OBD O O7 N N N 0 1.802 -3.735 2.205
45 OBC O O8 N N N 0 2.313 -1.392 2.992
46 OBE O O9 N N N 0 3.309 -2.33 0.747
47 PBF P P2 N N N 0 4.742 -3.065 0.756
48 OBH O O10 N N N 0 4.577 -4.57 0.208
49 OBG O O11 N N N 0 5.271 -3.098 2.138
50 O5' O O12 N N N 0 5.764 -2.258 -0.191
51 C5' C C31 N N N 0 7.147 -2.599 -0.312
52 C4' C C32 R N N 0 7.826 -1.635 -1.287
53 O4' O O13 N N N 0 7.843 -0.309 -0.732
54 C3' C C33 S N N 0 9.291 -2.059 -1.507
55 O3' O O14 N N N 0 9.525 -2.353 -2.886
56 C2' C C34 R N N 0 10.113 -0.822 -1.071
57 O2' O O15 N N N 0 11.205 -0.594 -1.964
58 C1' C C35 R N N 0 9.067 0.317 -1.174
59 N9 N N7 N Y N 0 9.426 1.429 -0.29
60 N7 N N8 N Y N 0 9.491 2.716 1.471
61 C2 C C36 N Y N 0 11.76 3.879 -1.628
62 N6 N N9 N N N 0 11.204 5.266 1.62
63 H4 H H4 N N N 0 -7.514 3.151 3.071
64 H1 H H1 N N N 0 8.273 0.988 1.496
65 H2 H H2 N N N 0 -5.77 4.806 -1.817
66 H3 H H3 N N N 0 -8.056 3.735 0.871
67 H5 H H5 N N N 0 -7.501 1.548 4.939
68 H6 H H6 N N N 0 -8.356 -0.737 4.607
69 H7 H H7 N N N 0 -9.223 -1.419 2.405
70 H8 H H8 N N N 0 -9.244 0.187 0.539
71 H9 H H9 N N N 0 -10.587 3.424 0.166
72 H10 H H10 N N N 0 -10.552 1.792 -1.842
73 H11 H H11 N N N 0 -9.864 -0.29 -2.903
74 H12 H H12 N N N 0 -9.146 -2.753 -4.671
75 H13 H H13 N N N 0 -9.511 -3.917 -3.375
76 H14 H H14 N N N 0 -10.562 -2.503 -3.623
77 H15 H H15 N N N 0 -6.588 -4.149 -3.243
78 H16 H H16 N N N 0 -6.773 -4.537 -1.516
79 H17 H H17 N N N 0 -8.176 -4.641 -2.607
80 H18 H H18 N N N 0 -5.94 -2.391 -0.763
81 H19 H H19 N N N 0 -5.255 0.097 1.683
82 H20 H H20 N N N 0 -5.708 -1.484 1.004
83 H21 H H21 N N N 0 -3.622 0.38 -0.213
84 H25 H H25 N N N 0 -1.244 -0.292 0.155
85 H22 H H22 N N N 0 -4.323 -2.379 -0.786
86 H23 H H23 N N N 0 -3.284 -2.146 1.467
87 H24 H H24 N N N 0 -2.592 0.616 2.038
88 H26 H H26 N N N 0 -1.936 -3.053 -0.416
89 H28 H H28 N N N 0 -0.858 -2.852 1.769
90 H27 H H27 N N N 0 -0.585 -1.21 2.399
91 H29 H H29 N N N 0 2.474 -0.468 2.755
92 H30 H H30 N N N 0 4.234 -4.624 -0.694
93 H31 H H31 N N N 0 7.626 -2.525 0.664
94 H32 H H32 N N N 0 7.238 -3.618 -0.686
95 H33 H H33 N N N 0 7.292 -1.632 -2.237
96 H34 H H34 N N N 0 9.536 -2.921 -0.887
97 H35 H H35 N N N 0 10.432 -2.625 -3.082
98 H36 H H36 N N N 0 10.468 -0.933 -0.046
99 H37 H H37 N N N 0 11.841 -1.321 -2.002
100 H38 H H38 N N N 0 8.973 0.659 -2.204
101 H39 H H39 N N N 0 12.343 4.123 -2.503
102 H40 H H40 N N N 0 10.691 5.069 2.419
103 H41 H H41 N N N 0 11.77 6.053 1.588



D3U : Chemical Bonds

Total Number of Bonds: 110
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAF CAE C C sing 1.51 N N
2 CAE CAG C C doub 1.38 N Y
3 CAE CAC C C sing 1.38 N Y
4 CAG CAH C C sing 1.38 N Y
5 CCC CCD C C doub 1.33 N N
6 CCC NAI C N sing 1.39 N N
7 CCD CCB C C sing 1.53 N N
8 CAD CAC C C sing 1.51 N N
9 CAC CAB C C doub 1.38 N Y
10 CAH NAI C N sing 1.39 N N
11 CAH CAA C C doub 1.4 N Y
12 NAI CAJ N C sing 1.47 N N
13 OAL CAK O C doub 1.21 N N
14 CCB CAJ C C sing 1.55 N N
15 CCB CCE C C sing 1.51 N N
16 CAB CAA C C sing 1.39 N Y
17 CAA NAR C N sing 1.4 N N
18 CAJ CAK C C sing 1.5 N N
19 CAJ CAQ C C sing 1.49 N N
20 CAK NAM C N sing 1.35 N N
21 CCE CCF C C doub 1.38 N Y
22 CCE CCJ C C sing 1.38 N Y
23 CCF CCG C C sing 1.38 N Y
24 CCJ CCI C C doub 1.38 N Y
25 NAR CAQ N C sing 1.35 N N
26 NAR CAS N C sing 1.47 N N
27 CAQ NAP C N doub 1.31 N N
28 NAM CAN N C sing 1.35 N N
29 CCG CCH C C doub 1.38 N Y
30 CCI CCH C C sing 1.38 N Y
31 OAU CAT O C sing 1.43 N N
32 CAS CAT C C sing 1.53 N N
33 NAP CAN N C sing 1.34 N N
34 CAN OAO C O doub 1.22 N N
35 CAT CAV C C sing 1.53 N N
36 O2' C2' O C sing 1.43 N N
37 CAV OAW C O sing 1.43 N N
38 CAV CAX C C sing 1.53 N N
39 OAY CAX O C sing 1.43 N N
40 OBG PBF O P doub 1.48 N N
41 C2' C3' C C sing 1.55 N N
42 C2' C1' C C sing 1.55 N N
43 CAX CAZ C C sing 1.53 N N
44 C8 N7 C N doub 1.3 N Y
45 C8 N9 C N sing 1.36 N Y
46 OBH PBF O P sing 1.61 N N
47 C3' O3' C O sing 1.43 N N
48 C3' C4' C C sing 1.54 N N
49 N7 C5 N C sing 1.36 N Y
50 PBF O5' P O sing 1.61 N N
51 PBF OBE P O sing 1.61 N N
52 N9 C1' N C sing 1.47 N N
53 N9 C4 N C sing 1.37 N Y
54 CAZ OBA C O sing 1.43 N N
55 C1' O4' C O sing 1.44 N N
56 C5 C4 C C doub 1.4 N Y
57 C5 C6 C C sing 1.41 N Y
58 N6 C6 N C sing 1.38 N N
59 C4 N3 C N sing 1.33 N Y
60 C6 N1 C N doub 1.33 N Y
61 O5' C5' O C sing 1.43 N N
62 OBE PBB O P sing 1.61 N N
63 OBA PBB O P sing 1.61 N N
64 C4' O4' C O sing 1.44 N N
65 C4' C5' C C sing 1.53 N N
66 N3 C2 N C doub 1.32 N Y
67 N1 C2 N C sing 1.32 N Y
68 PBB OBD P O doub 1.48 N N
69 PBB OBC P O sing 1.61 N N
70 C8 H1 C H sing 1.08 N N
71 NAM H2 N H sing 0.97 N N
72 CCB H3 C H sing 1.09 N N
73 CCF H4 C H sing 1.08 N N
74 CCG H5 C H sing 1.08 N N
75 CCH H6 C H sing 1.08 N N
76 CCI H7 C H sing 1.08 N N
77 CCJ H8 C H sing 1.08 N N
78 CCD H9 C H sing 1.08 N N
79 CCC H10 C H sing 1.08 N N
80 CAG H11 C H sing 1.08 N N
81 CAF H12 C H sing 1.09 N N
82 CAF H13 C H sing 1.09 N N
83 CAF H14 C H sing 1.09 N N
84 CAD H15 C H sing 1.09 N N
85 CAD H16 C H sing 1.09 N N
86 CAD H17 C H sing 1.09 N N
87 CAB H18 C H sing 1.08 N N
88 CAS H19 C H sing 1.09 N N
89 CAS H20 C H sing 1.09 N N
90 CAT H21 C H sing 1.09 N N
91 OAU H22 O H sing 0.97 N N
92 CAV H23 C H sing 1.09 N N
93 OAW H24 O H sing 0.97 N N
94 CAX H25 C H sing 1.09 N N
95 OAY H26 O H sing 0.97 N N
96 CAZ H27 C H sing 1.09 N N
97 CAZ H28 C H sing 1.09 N N
98 OBC H29 O H sing 0.97 N N
99 OBH H30 O H sing 0.97 N N
100 C5' H31 C H sing 1.09 N N
101 C5' H32 C H sing 1.09 N N
102 C4' H33 C H sing 1.09 N N
103 C3' H34 C H sing 1.09 N N
104 O3' H35 O H sing 0.97 N N
105 C2' H36 C H sing 1.09 N N
106 O2' H37 O H sing 0.97 N N
107 C1' H38 C H sing 1.09 N N
108 C2 H39 C H sing 1.08 N N
109 N6 H40 N H sing 0.97 N N
110 N6 H41 N H sing 0.97 N N



D3U : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
D3U 6k3e Open in New Window Bound ligand 1 1