Chemical Components in the PDB

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UCA : Summary

Code

UCA

One-letter code

X

Molecule name

S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-[(3aS,4S,7aS)-7a-methyl-1,5-bis(oxidanylidene)-2,3,3a,4,6,7-hexahydroinden-4-yl]propanethioate

Synonyms

HIP-CoA

Systematic names

ProgramVersionName
ACDLabs 12.01 S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxooctahydro-1H-inden-4-yl]propanethioate (non-preferred name)
OpenEye OEToolkits 1.7.6 S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-[(3aS,4S,7aS)-7a-methyl-1,5-bis(oxidanylidene)-2,3,3a,4,6,7-hexahydroinden-4-yl]propanethioate

Formula

C34 H52 N7 O19 P3 S

Formal charge

0

Molecular weight

987.798 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1CCC2C1(C)CCC(=O)C2CCC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC5OC(n4cnc3c(ncnc34)N)C(O)C5OP(=O)(O)O
SMILES CACTVS 3.385 CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSC(=O)CC[CH]4[CH]5CCC(=O)[C]5(C)CCC4=O
SMILES OpenEye OEToolkits 1.7.6 CC12CCC(=O)C(C1CCC2=O)CCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)OP(=O)(O)O)O
Canonical SMILES CACTVS 3.385 CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)CC[C@H]4[C@@H]5CCC(=O)[C@@]5(C)CCC4=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@]12CCC(=O)[C@H]([C@@H]1CCC2=O)CCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)OP(=O)(O)O)O

IUPAC InChI

InChI=1S/C34H52N7O19P3S/c1-33(2,28(47)31(48)37-11-9-23(44)36-12-13-64-24(45)7-4-18-19-5-6-22(43)34(19,3)10-8-20(18)42)15-57-63(54,55)60-62(52,53)56-14-21-27(59-61(49,50)51)26(46)32(58-21)41-17-40-25-29(35)38-16-39-30(25)41/h16-19,21,26-28,32,46-47H,4-15H2,1-3H3,(H,36,44)(H,37,48)(H,52,53)(H,54,55)(H2,35,38,39)(H2,49,50,51)/t18-,19-,21+,26+,27+,28-,32+,34-/m0/s1

IUPAC InChI key

IWNWMTZIJPUDPV-MDQHZGBLSA-N
UCA

wwPDB Information

Atom count

116 (64 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-08-27

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



UCA : Atoms of Molecule

Total Number of Atoms: 116
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 -8.5 -5.239 -0.583
2 C5 C C2 N Y N 0 -7.601 -6.077 0.097
3 C6 C C3 N Y N 0 -7.543 -7.431 -0.277
4 C8 C C4 N Y N 0 -7.394 -4.089 0.939
5 N1 N N1 N Y N 0 -8.34 -7.852 -1.253
6 N3 N N2 N Y N 0 -9.259 -5.752 -1.547
7 OAG O O1 N N N 0 13.41 -3.304 -0.824
8 CBT C C5 N N N 0 14.534 -2.971 -0.53
9 CBA C C6 N N N 0 15.683 -3.93 -0.726
10 CBD C C7 N N N 0 16.577 -3.95 0.527
11 CCI C C8 S N N 0 16.929 -2.513 0.859
12 CAC C C9 N N N 0 17.511 -1.827 -0.378
13 CBU C C10 N N N 0 17.85 -2.312 2.029
14 OAH O O2 N N N 0 18.739 -3.046 2.387
15 CAZ C C11 N N N 0 17.435 -0.994 2.671
16 CBC C C12 N N N 0 16.191 -0.491 1.891
17 CCD C C13 S N N 0 15.628 -1.787 1.295
18 CCC C C14 S N N 0 14.794 -1.583 0.031
19 CBB C C15 N N N 0 13.47 -0.899 0.379
20 CAY C C16 N N N 0 12.665 -0.666 -0.901
21 CBS C C17 N N N 0 11.361 0.007 -0.559
22 OAF O O3 N N N 0 11.101 0.274 0.596
23 SBQ S S1 N N N 0 10.247 0.396 -1.799
24 CAW C C18 N N N 0 8.931 1.153 -0.814
25 CAU C C19 N N N 0 7.792 1.592 -1.736
26 NBJ N N3 N N N 0 6.726 2.204 -0.938
27 CBR C C20 N N N 0 5.615 2.669 -1.542
28 OAE O O4 N N N 0 5.496 2.58 -2.746
29 CAX C C21 N N N 0 4.519 3.299 -0.721
30 CAV C C22 N N N 0 3.38 3.738 -1.643
31 NBK N N4 N N N 0 2.314 4.351 -0.846
32 CBV C C23 N N N 0 1.203 4.815 -1.45
33 OAI O O5 N N N 0 1.123 4.812 -2.66
34 CBZ C C24 R N N 0 0.058 5.34 -0.621
35 OAM O O6 N N N 0 0.484 5.497 0.734
36 CCH C C25 N N N 0 -1.108 4.351 -0.678
37 CAA C C26 N N N 0 -1.66 4.294 -2.103
38 CAB C C27 N N N 0 -0.618 2.961 -0.265
39 CBF C C28 N N N 0 -2.211 4.807 0.279
40 OBM O O7 N N N 0 -3.3 3.883 0.226
41 PCL P P1 N N N 0 -4.637 4.052 1.107
42 OAR O O8 N N N 0 -4.274 4.166 2.537
43 OAL O O9 N N N 0 -5.419 5.381 0.645
44 OBP O O10 N N N 0 -5.585 2.769 0.894
45 PCK P P2 N N N 0 -6.863 2.18 1.678
46 OAQ O O11 N N N 0 -7.8 3.282 1.992
47 OAK O O12 N N N 0 -6.378 1.482 3.045
48 O5' O O13 N N N 0 -7.605 1.091 0.753
49 C5' C C29 N N N 0 -8.833 0.463 1.124
50 C4' C C30 R N N 0 -9.259 -0.513 0.024
51 O4' O O14 N N N 0 -8.323 -1.601 -0.053
52 C3' C C31 S N N 0 -10.635 -1.117 0.364
53 O3' O O15 N N N 0 -11.585 -0.802 -0.657
54 PCJ P P3 N N N 0 -12.933 0.032 -0.374
55 OAO O O16 N N N 0 -13.704 -0.626 0.704
56 OAP O O17 N N N 0 -12.552 1.53 0.077
57 OAJ O O18 N N N 0 -13.822 0.085 -1.715
58 C2' C C32 R N N 0 -10.379 -2.642 0.414
59 O2' O O19 N N N 0 -11.451 -3.36 -0.201
60 C1' C C33 R N N 0 -9.075 -2.78 -0.412
61 N9 N N5 N Y N 0 -8.347 -3.993 -0.03
62 N7 N N6 N Y N 0 -6.961 -5.314 1.015
63 C2 C C34 N Y N 0 -9.17 -7.026 -1.864
64 N6 N N7 N N N 0 -6.676 -8.304 0.356
65 H1 H H1 N N N 0 -7.051 -3.271 1.555
66 H4 H H4 N N N 0 15.291 -4.931 -0.906
67 H5 H H5 N N N 0 16.274 -3.616 -1.586
68 H6 H H6 N N N 0 16.037 -4.401 1.36
69 H7 H H7 N N N 0 17.485 -4.517 0.324
70 H8 H H8 N N N 0 16.771 -1.831 -1.178
71 H9 H H9 N N N 0 17.775 -0.798 -0.133
72 H10 H H10 N N N 0 18.403 -2.362 -0.705
73 H11 H H11 N N N 0 17.179 -1.153 3.719
74 H12 H H12 N N N 0 18.244 -0.268 2.591
75 H13 H H13 N N N 0 15.469 -0.034 2.568
76 H14 H H14 N N N 0 16.483 0.208 1.107
77 H15 H H15 N N N 0 15.087 -2.365 2.044
78 H16 H H16 N N N 0 15.347 -0.984 -0.693
79 H17 H H17 N N N 0 12.9 -1.536 1.056
80 H18 H H18 N N N 0 13.67 0.057 0.862
81 H19 H H19 N N N 0 13.236 -0.03 -1.578
82 H20 H H20 N N N 0 12.465 -1.622 -1.384
83 H22 H H22 N N N 0 8.555 0.428 -0.092
84 H23 H H23 N N N 0 9.326 2.02 -0.285
85 H24 H H24 N N N 0 8.167 2.316 -2.458
86 H25 H H25 N N N 0 7.397 0.724 -2.264
87 H26 H H26 N N N 0 6.821 2.276 0.025
88 H27 H H27 N N N 0 4.143 2.574 0.001
89 H28 H H28 N N N 0 4.914 4.167 -0.193
90 H29 H H29 N N N 0 3.755 4.463 -2.365
91 H30 H H30 N N N 0 2.985 2.871 -2.172
92 H31 H H31 N N N 0 2.409 4.422 0.117
93 H32 H H32 N N N 0 -0.264 6.304 -1.015
94 H33 H H33 N N N 0 0.785 4.677 1.149
95 H34 H H34 N N N 0 -0.898 3.895 -2.773
96 H35 H H35 N N N 0 -2.539 3.65 -2.127
97 H36 H H36 N N N 0 -1.937 5.298 -2.426
98 H37 H H37 N N N 0 -0.224 3.001 0.751
99 H38 H H38 N N N 0 -1.448 2.256 -0.306
100 H39 H H39 N N N 0 0.168 2.636 -0.947
101 H40 H H40 N N N 0 -1.817 4.847 1.295
102 H41 H H41 N N N 0 -2.56 5.797 -0.015
103 H42 H H42 N N N 0 -5.688 5.376 -0.284
104 H43 H H43 N N N 0 -5.76 0.749 2.915
105 H44 H H44 N N N 0 -8.695 -0.081 2.058
106 H45 H H45 N N N 0 -9.605 1.221 1.255
107 H46 H H46 N N N 0 -9.305 0.005 -0.933
108 H47 H H47 N N N 0 -10.983 -0.754 1.332
109 H48 H H48 N N N 0 -12.044 2.023 -0.583
110 H49 H H49 N N N 0 -14.651 0.574 -1.617
111 H50 H H50 N N N 0 -10.227 -2.978 1.44
112 H51 H H51 N N N 0 -11.336 -4.32 -0.194
113 H52 H H52 N N N 0 -9.296 -2.783 -1.48
114 H53 H H53 N N N 0 -9.8 -7.411 -2.652
115 H54 H H54 N N N 0 -6.099 -7.984 1.067
116 H55 H H55 N N N 0 -6.645 -9.236 0.089



UCA : Chemical Bonds

Total Number of Bonds: 120
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C4 C5 C C doub 1.4 N Y
2 C4 N3 C N sing 1.33 N Y
3 C4 N9 C N sing 1.37 N Y
4 C5 C6 C C sing 1.41 N Y
5 C5 N7 C N sing 1.35 N Y
6 C6 N1 C N doub 1.33 N Y
7 C6 N6 C N sing 1.38 N N
8 C8 N9 C N sing 1.36 N Y
9 C8 N7 C N doub 1.3 N Y
10 N1 C2 N C sing 1.32 N Y
11 N3 C2 N C doub 1.32 N Y
12 OAG CBT O C doub 1.21 N N
13 CBT CBA C C sing 1.51 N N
14 CBT CCC C C sing 1.52 N N
15 CBA CBD C C sing 1.54 N N
16 CBD CCI C C sing 1.52 N N
17 CCI CAC C C sing 1.53 N N
18 CCI CBU C C sing 1.5 N N
19 CCI CCD C C sing 1.55 N N
20 CBU OAH C O doub 1.21 N N
21 CBU CAZ C C sing 1.52 N N
22 CAZ CBC C C sing 1.55 N N
23 CBC CCD C C sing 1.53 N N
24 CCD CCC C C sing 1.53 N N
25 CCC CBB C C sing 1.53 N N
26 CBB CAY C C sing 1.53 N N
27 CAY CBS C C sing 1.51 N N
28 CBS OAF C O doub 1.21 N N
29 CBS SBQ C S sing 1.71 N N
30 SBQ CAW S C sing 1.81 N N
31 CAW CAU C C sing 1.53 N N
32 CAU NBJ C N sing 1.47 N N
33 NBJ CBR N C sing 1.35 N N
34 CBR OAE C O doub 1.21 N N
35 CBR CAX C C sing 1.51 N N
36 CAX CAV C C sing 1.53 N N
37 CAV NBK C N sing 1.47 N N
38 NBK CBV N C sing 1.35 N N
39 CBV OAI C O doub 1.21 N N
40 CBV CBZ C C sing 1.51 N N
41 CBZ OAM C O sing 1.43 N N
42 CBZ CCH C C sing 1.53 N N
43 CCH CAA C C sing 1.53 N N
44 CCH CAB C C sing 1.53 N N
45 CCH CBF C C sing 1.53 N N
46 CBF OBM C O sing 1.43 N N
47 OBM PCL O P sing 1.61 N N
48 PCL OAR P O doub 1.48 N N
49 PCL OAL P O sing 1.61 N N
50 PCL OBP P O sing 1.61 N N
51 OBP PCK O P sing 1.61 N N
52 PCK OAQ P O doub 1.48 N N
53 PCK OAK P O sing 1.61 N N
54 PCK O5' P O sing 1.61 N N
55 O5' C5' O C sing 1.43 N N
56 C5' C4' C C sing 1.53 N N
57 C4' O4' C O sing 1.44 N N
58 C4' C3' C C sing 1.54 N N
59 O4' C1' O C sing 1.44 N N
60 C3' O3' C O sing 1.43 N N
61 C3' C2' C C sing 1.55 N N
62 O3' PCJ O P sing 1.61 N N
63 PCJ OAO P O doub 1.48 N N
64 PCJ OAP P O sing 1.61 N N
65 PCJ OAJ P O sing 1.61 N N
66 C2' O2' C O sing 1.43 N N
67 C2' C1' C C sing 1.55 N N
68 C1' N9 C N sing 1.47 N N
69 C8 H1 C H sing 1.08 N N
70 CBA H4 C H sing 1.09 N N
71 CBA H5 C H sing 1.09 N N
72 CBD H6 C H sing 1.09 N N
73 CBD H7 C H sing 1.09 N N
74 CAC H8 C H sing 1.09 N N
75 CAC H9 C H sing 1.09 N N
76 CAC H10 C H sing 1.09 N N
77 CAZ H11 C H sing 1.09 N N
78 CAZ H12 C H sing 1.09 N N
79 CBC H13 C H sing 1.09 N N
80 CBC H14 C H sing 1.09 N N
81 CCD H15 C H sing 1.09 N N
82 CCC H16 C H sing 1.09 N N
83 CBB H17 C H sing 1.09 N N
84 CBB H18 C H sing 1.09 N N
85 CAY H19 C H sing 1.09 N N
86 CAY H20 C H sing 1.09 N N
87 CAW H22 C H sing 1.09 N N
88 CAW H23 C H sing 1.09 N N
89 CAU H24 C H sing 1.09 N N
90 CAU H25 C H sing 1.09 N N
91 NBJ H26 N H sing 0.97 N N
92 CAX H27 C H sing 1.09 N N
93 CAX H28 C H sing 1.09 N N
94 CAV H29 C H sing 1.09 N N
95 CAV H30 C H sing 1.09 N N
96 NBK H31 N H sing 0.97 N N
97 CBZ H32 C H sing 1.09 N N
98 OAM H33 O H sing 0.97 N N
99 CAA H34 C H sing 1.09 N N
100 CAA H35 C H sing 1.09 N N
101 CAA H36 C H sing 1.09 N N
102 CAB H37 C H sing 1.09 N N
103 CAB H38 C H sing 1.09 N N
104 CAB H39 C H sing 1.09 N N
105 CBF H40 C H sing 1.09 N N
106 CBF H41 C H sing 1.09 N N
107 OAL H42 O H sing 0.97 N N
108 OAK H43 O H sing 0.97 N N
109 C5' H44 C H sing 1.09 N N
110 C5' H45 C H sing 1.09 N N
111 C4' H46 C H sing 1.09 N N
112 C3' H47 C H sing 1.09 N N
113 OAP H48 O H sing 0.97 N N
114 OAJ H49 O H sing 0.97 N N
115 C2' H50 C H sing 1.09 N N
116 O2' H51 O H sing 0.97 N N
117 C1' H52 C H sing 1.09 N N
118 C2 H53 C H sing 1.08 N N
119 N6 H54 N H sing 0.97 N N
120 N6 H55 N H sing 0.97 N N



UCA : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
UCA 4w97 Open in New Window Bound ligand 1 1