Chemical Components in the PDB

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CIC : Summary

Code

CIC

One-letter code

X

Molecule name

CITRYL-THIOETHER-COENZYME *A

Systematic names

ProgramVersionName
ACDLabs 10.04 (2S)-2-{(12R,16S,18R)-20-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-12,16,18-trihydroxy-13,13-dimethyl-16,18-dioxido-7,11-dioxo-15,17,19-trioxa-3-thia-6,10-diaza-16,18-diphosphaicos-1-yl}-2-hydroxybutanedioic acid (non-preferred name)
OpenEye OEToolkits 1.5.0 (2S)-2-[2-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-2-hydroxy-3,3-dimethyl-butanoyl]amino]propanoylamino]ethylsulfanyl]ethyl]-2-hydroxy-butanedioic acid

Formula

C27 H44 N7 O21 P3 S

Formal charge

0

Molecular weight

927.659 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(O)(CC(=O)O)CCSCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
SMILES CACTVS 3.341 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)NCCSCC[C](O)(CC(O)=O)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSCCC(CC(=O)O)(C(=O)O)O)O
Canonical SMILES CACTVS 3.341 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)NCCSCC[C@@](O)(CC(O)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(C)(CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSCC[C@@](CC(=O)O)(C(=O)O)O)O

IUPAC InChI

InChI=1S/C27H44N7O21P3S/c1-26(2,20(39)23(40)30-5-3-15(35)29-6-8-59-7-4-27(43,25(41)42)9-16(36)37)11-52-58(49,50)55-57(47,48)51-10-14-19(54-56(44,45)46)18(38)24(53-14)34-13-33-17-21(28)31-12-32-22(17)34/h12-14,18-20,24,38-39,43H,3-11H2,1-2H3,(H,29,35)(H,30,40)(H,36,37)(H,41,42)(H,47,48)(H,49,50)(H2,28,31,32)(H2,44,45,46)/t14-,18-,19-,20+,24-,27-/m1/s1

IUPAC InChI key

VPFUWJMPUQBRCJ-QVYRMQCDSA-N
CIC

wwPDB Information

Atom count

103 (59 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAC

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



CIC : 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 N1A N AN1 N Y N 0 -7.837 -2.031 -6.949
2 C2A C AC2 N Y N 0 -7.039 -1.925 -7.995
3 N3A N AN3 N Y N 0 -5.782 -1.547 -7.89
4 C4A C AC4 N Y N 0 -5.262 -1.248 -6.704
5 C5A C AC5 N Y N 0 -6.069 -1.351 -5.559
6 C6A C AC6 N Y N 0 -7.404 -1.758 -5.722
7 N6A N AN6 N N N 0 -8.248 -1.872 -4.632
8 N7A N AN7 N Y N 0 -5.303 -1.001 -4.498
9 C8A C AC8 N Y N 0 -4.105 -0.702 -4.908
10 N9A N AN9 N Y N 0 -4.028 -0.842 -6.262
11 C1B C AC1* R N N 0 -2.847 -0.598 -7.093
12 C2B C AC2* R N N 0 -2.747 0.899 -7.479
13 O2B O AO2* N N N 0 -3.51 1.174 -8.655
14 C3B C AC3* S N N 0 -1.229 1.062 -7.755
15 O3B O AO3* N N N 0 -0.963 0.979 -9.156
16 P3B P AP3* N N N 0 -0.252 2.36 -9.578
17 O7A O AO7 N N N 0 1.004 2.522 -8.814
18 O8A O AO8 N N N 0 0.077 2.335 -11.154
19 O9A O AO9 N N N 0 -1.238 3.591 -9.256
20 C4B C AC4* R N N 0 -0.583 -0.118 -7.005
21 O4B O AO4* N N N 0 -1.638 -0.834 -6.34
22 C5B C AC5* N N N 0 0.419 0.405 -5.974
23 O5B O AO5* N N N 0 1.007 -0.696 -5.279
24 P1A P AP1 R N N 0 2.045 -0.075 -4.217
25 O1A O AO1 N N N 0 3.078 0.703 -4.936
26 O2A O AO2 N N N 0 1.258 0.889 -3.197
27 O3A O AO3 N N N 0 2.748 -1.267 -3.395
28 P2A P AP2 S N N 0 3.768 -0.578 -2.357
29 O4A O AO4 N N N 0 4.775 0.208 -3.104
30 O5A O AO5 N N N 0 2.952 0.394 -1.368
31 O6A O AO6 N N N 0 4.51 -1.719 -1.496
32 CBP C PC11 N N N 0 6.137 -2.08 0.253
33 CCP C PC12 N N N 0 5.397 -1.048 -0.599
34 CDP C PC13 N N N 0 5.125 -2.9 1.055
35 CEP C PC14 N N N 0 6.941 -3.011 -0.656
36 CAP C PC10 R N N 0 7.087 -1.361 1.214
37 OAP O PO10 N N N 0 8.115 -0.707 0.467
38 C9P C PC9 N N N 0 6.317 -0.34 2.011
39 O9P O PO9 N N N 0 6.483 0.842 1.801
40 N8P N PN8 N N N 0 5.444 -0.741 2.956
41 C7P C PC7 N N N 0 4.756 0.25 3.786
42 C6P C PC6 N N N 0 3.828 -0.463 4.771
43 C5P C PC5 N N N 0 3.121 0.556 5.624
44 O5P O PO5 N N N 0 3.336 1.739 5.461
45 N4P N PN4 N N N 0 2.248 0.155 6.57
46 C3P C PC3 N N N 0 1.559 1.147 7.399
47 C2P C PC2 N N N 0 0.632 0.433 8.385
48 S1P S PS1 N N N 0 -0.219 1.661 9.412
49 C1P C PC1 N N N 0 -1.219 0.562 10.453
50 C1 C C1 N N N 0 -2.048 1.399 11.43
51 C2 C C2 S N N 0 -2.891 0.473 12.308
52 O2 O O2 N N N 0 -2.03 -0.401 13.041
53 C3 C C3 N N N 0 -3.812 -0.342 11.437
54 O31 O O31 N N N 0 -3.739 -1.548 11.444
55 O32 O O32 N N N 0 -4.713 0.27 10.654
56 C4 C C4 N N N 0 -3.72 1.309 13.284
57 C5 C C5 N N N 0 -4.55 0.396 14.149
58 O51 O O51 N N N 0 -4.486 -0.8 13.999
59 O52 O O52 N N N 0 -5.362 0.913 15.085
60 H2A H AH2 N N N 0 -7.432 -2.157 -8.974
61 H61A H AH61 N N N 0 -9.168 -2.154 -4.757
62 H62A H AH62 N N N 0 -7.921 -1.67 -3.741
63 H8A H AH8 N N N 0 -3.292 -0.389 -4.271
64 H1B H AH1* N N N 0 -2.871 -1.224 -7.986
65 H2B H AH2* N N N 0 -3.064 1.535 -6.653
66 HO2A H AHO2 N N N 0 -4.431 0.965 -8.446
67 H3B H AH3* N N N 0 -0.868 2.01 -7.355
68 HOA8 H 8HOA N N N 0 0.5 3.178 -11.365
69 HOA9 H 9HOA N N N 0 -2.043 3.448 -9.773
70 H4B H AH4* N N N 0 -0.078 -0.775 -7.712
71 H51A H AH51 N N N 0 -0.094 1.051 -5.263
72 H52A H AH52 N N N 0 1.199 0.972 -6.482
73 HOA2 H 2HOA N N N 0 0.596 0.343 -2.751
74 HOA5 H 5HOA N N N 0 2.308 -0.156 -0.902
75 H121 H 1H12 N N N 0 4.824 -0.384 0.049
76 H122 H 2H12 N N N 0 6.118 -0.463 -1.17
77 H131 H 1H13 N N N 0 4.47 -2.227 1.609
78 H132 H 2H13 N N N 0 4.529 -3.508 0.374
79 H133 H 3H13 N N N 0 5.654 -3.549 1.753
80 H141 H 1H14 N N N 0 7.707 -2.437 -1.177
81 H142 H 2H14 N N N 0 7.414 -3.787 -0.055
82 H143 H 3H14 N N N 0 6.274 -3.472 -1.385
83 H10 H H10 N N N 0 7.536 -2.087 1.891
84 HO1 H HO1 N N N 0 7.676 -0.075 -0.117
85 HN8 H HN8 N N N 0 5.271 -1.686 3.087
86 H71 H 1H7 N N N 0 5.491 0.835 4.338
87 H72 H 2H7 N N N 0 4.169 0.912 3.149
88 H61 H 1H6 N N N 0 3.093 -1.048 4.219
89 H62 H 2H6 N N N 0 4.415 -1.125 5.408
90 HN4 H HN4 N N N 0 2.075 -0.789 6.701
91 H31 H 1H3 N N N 0 2.295 1.732 7.952
92 H32 H 2H3 N N N 0 0.972 1.809 6.763
93 H21 H 1H2 N N N 0 -0.103 -0.151 7.833
94 H22 H 2H2 N N N 0 1.219 -0.228 9.022
95 H11 H 1H1 N N N 0 -1.885 -0.027 9.824
96 H12 H 2H1 N N N 0 -0.563 -0.103 11.013
97 H111 H H11 N N N 0 -1.381 1.989 12.059
98 H123 H H12 N N N 0 -2.704 2.066 10.87
99 HO2 H HO2 N N N 0 -1.459 0.159 13.583
100 HO32 H 2HO3 N N N 0 -5.304 -0.252 10.096
101 H41 H H41 N N N 0 -3.053 1.899 13.913
102 H42 H H42 N N N 0 -4.376 1.976 12.724
103 HO52 H 2HO5 N N N 0 -5.894 0.328 15.64



CIC : Chemical Bonds

Total Number of Bonds: 105
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1A C2A N C sing 1.32 N Y
2 N1A C6A N C doub 1.33 N Y
3 C2A N3A C N doub 1.32 N Y
4 C2A H2A C H sing 1.08 N N
5 N3A C4A N C sing 1.33 N Y
6 C4A C5A C C doub 1.4 N Y
7 C4A N9A C N sing 1.37 N Y
8 C5A C6A C C sing 1.41 N Y
9 C5A N7A C N sing 1.35 N Y
10 C6A N6A C N sing 1.38 N N
11 N6A H61A N H sing 0.97 N N
12 N6A H62A N H sing 0.97 N N
13 N7A C8A N C doub 1.3 N Y
14 C8A N9A C N sing 1.36 N Y
15 C8A H8A C H sing 1.08 N N
16 N9A C1B N C sing 1.46 N N
17 C1B C2B C C sing 1.55 N N
18 C1B O4B C O sing 1.44 N N
19 C1B H1B C H sing 1.09 N N
20 C2B O2B C O sing 1.43 N N
21 C2B C3B C C sing 1.55 N N
22 C2B H2B C H sing 1.09 N N
23 O2B HO2A O H sing 0.97 N N
24 C3B O3B C O sing 1.43 N N
25 C3B C4B C C sing 1.54 N N
26 C3B H3B C H sing 1.09 N N
27 O3B P3B O P sing 1.61 N N
28 P3B O7A P O doub 1.48 N N
29 P3B O8A P O sing 1.61 N N
30 P3B O9A P O sing 1.61 N N
31 O8A HOA8 O H sing 0.97 N N
32 O9A HOA9 O H sing 0.97 N N
33 C4B O4B C O sing 1.44 N N
34 C4B C5B C C sing 1.53 N N
35 C4B H4B C H sing 1.09 N N
36 C5B O5B C O sing 1.43 N N
37 C5B H51A C H sing 1.09 N N
38 C5B H52A C H sing 1.09 N N
39 O5B P1A O P sing 1.61 N N
40 P1A O1A P O doub 1.48 N N
41 P1A O2A P O sing 1.61 N N
42 P1A O3A P O sing 1.61 N N
43 O2A HOA2 O H sing 0.97 N N
44 O3A P2A O P sing 1.61 N N
45 P2A O4A P O doub 1.48 N N
46 P2A O5A P O sing 1.61 N N
47 P2A O6A P O sing 1.61 N N
48 O5A HOA5 O H sing 0.97 N N
49 O6A CCP O C sing 1.43 N N
50 CBP CCP C C sing 1.53 N N
51 CBP CDP C C sing 1.53 N N
52 CBP CEP C C sing 1.53 N N
53 CBP CAP C C sing 1.53 N N
54 CCP H121 C H sing 1.09 N N
55 CCP H122 C H sing 1.09 N N
56 CDP H131 C H sing 1.09 N N
57 CDP H132 C H sing 1.09 N N
58 CDP H133 C H sing 1.09 N N
59 CEP H141 C H sing 1.09 N N
60 CEP H142 C H sing 1.09 N N
61 CEP H143 C H sing 1.09 N N
62 CAP OAP C O sing 1.43 N N
63 CAP C9P C C sing 1.51 N N
64 CAP H10 C H sing 1.09 N N
65 OAP HO1 O H sing 0.97 N N
66 C9P O9P C O doub 1.21 N N
67 C9P N8P C N sing 1.35 N N
68 N8P C7P N C sing 1.46 N N
69 N8P HN8 N H sing 0.97 N N
70 C7P C6P C C sing 1.53 N N
71 C7P H71 C H sing 1.09 N N
72 C7P H72 C H sing 1.09 N N
73 C6P C5P C C sing 1.51 N N
74 C6P H61 C H sing 1.09 N N
75 C6P H62 C H sing 1.09 N N
76 C5P O5P C O doub 1.21 N N
77 C5P N4P C N sing 1.35 N N
78 N4P C3P N C sing 1.46 N N
79 N4P HN4 N H sing 0.97 N N
80 C3P C2P C C sing 1.53 N N
81 C3P H31 C H sing 1.09 N N
82 C3P H32 C H sing 1.09 N N
83 C2P S1P C S sing 1.81 N N
84 C2P H21 C H sing 1.09 N N
85 C2P H22 C H sing 1.09 N N
86 S1P C1P S C sing 1.81 N N
87 C1P C1 C C sing 1.53 N N
88 C1P H11 C H sing 1.09 N N
89 C1P H12 C H sing 1.09 N N
90 C1 C2 C C sing 1.53 N N
91 C1 H111 C H sing 1.09 N N
92 C1 H123 C H sing 1.09 N N
93 C2 O2 C O sing 1.43 N N
94 C2 C3 C C sing 1.51 N N
95 C2 C4 C C sing 1.53 N N
96 O2 HO2 O H sing 0.97 N N
97 C3 O31 C O doub 1.21 N N
98 C3 O32 C O sing 1.34 N N
99 O32 HO32 O H sing 0.97 N N
100 C4 C5 C C sing 1.51 N N
101 C4 H41 C H sing 1.09 N N
102 C4 H42 C H sing 1.09 N N
103 C5 O51 C O doub 1.21 N N
104 C5 O52 C O sing 1.34 N N
105 O52 HO52 O H sing 0.97 N N



CIC : Used in PDB Entries

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