Chemical Components in the PDB

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HXC : Summary

Code

HXC

One-letter code

X

Molecule name

HEXANOYL-COENZYME A

Systematic names

ProgramVersionName
ACDLabs 10.04 S-{(9R,13R,15S)-17-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-9,13,15-trihydroxy-10,10-dimethyl-13,15-dioxido-4,8-dioxo-12,14,16-trioxa-3,7-diaza-13,15-diphosphaheptadec-1-yl} hexanethioate (non-preferred name)
OpenEye OEToolkits 1.5.0 S-[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]ethyl] hexanethioate

Formula

C27 H46 N7 O17 P3 S

Formal charge

0

Molecular weight

865.677 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)CCCCC
SMILES CACTVS 3.341 CCCCCC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
SMILES OpenEye OEToolkits 1.5.0 CCCCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
Canonical SMILES CACTVS 3.341 CCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(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
Canonical SMILES OpenEye OEToolkits 1.5.0 CCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(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)O

IUPAC InChI

InChI=1S/C27H46N7O17P3S/c1-4-5-6-7-18(36)55-11-10-29-17(35)8-9-30-25(39)22(38)27(2,3)13-48-54(45,46)51-53(43,44)47-12-16-21(50-52(40,41)42)20(37)26(49-16)34-15-33-19-23(28)31-14-32-24(19)34/h14-16,20-22,26,37-38H,4-13H2,1-3H3,(H,29,35)(H,30,39)(H,43,44)(H,45,46)(H2,28,31,32)(H2,40,41,42)/t16-,20-,21-,22+,26-/m1/s1

IUPAC InChI key

OEXFMSFODMQEPE-HDRQGHTBSA-N
HXC

wwPDB Information

Atom count

101 (55 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



HXC : Atoms of Molecule

Total Number of Atoms: 101
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C2 N Y N 0 4.183 -2.155 -11.582
2 C4 C C4 N Y N 0 2.613 -1.937 -9.917
3 C5 C C5 N Y N 0 2.331 -3.31 -10.018
4 C6 C C6 N Y N 0 3.042 -4.065 -10.966
5 C8 C C8 N Y N 0 1.049 -2.5 -8.468
6 N9 N N9 N Y N 0 1.794 -1.454 -8.929
7 N7 N N7 N Y N 0 1.366 -3.587 -9.109
8 N3 N N3 N Y N 0 3.541 -1.408 -10.708
9 N1 N N1 N Y N 0 3.949 -3.448 -11.717
10 N6 N N6 N N N 0 2.804 -5.42 -11.115
11 C1' C C1' R N N 0 1.726 -0.069 -8.458
12 C2' C C2' R N N 0 0.607 0.708 -9.198
13 O2' O O2' N N N 0 1.092 1.252 -10.427
14 C3' C C3' S N N 0 0.273 1.837 -8.187
15 O3' O O3' N N N 0 0.951 3.043 -8.543
16 C4' C C4' R N N 0 0.79 1.297 -6.839
17 O4' O O4' N N N 0 1.312 -0.021 -7.076
18 C5' C C5' N N N 0 -0.359 1.228 -5.832
19 O5' O O5' N N N 0 0.127 0.72 -4.588
20 P1 P P1 S N N 0 -1.127 0.675 -3.581
21 O11 O O11 N N N 0 -2.174 -0.211 -4.137
22 O12 O O12 N N N 0 -1.722 2.159 -3.398
23 O6 O O6 N N N 0 -0.648 0.108 -2.152
24 P2 P P2 R N N 0 -1.946 0.091 -1.199
25 O21 O O21 N N N 0 -2.981 -0.785 -1.792
26 O22 O O22 N N N 0 -2.528 1.585 -1.056
27 O7 O O7 N N N 0 -1.538 -0.467 0.253
28 CPB C CPB N N N 0 -2.726 -0.458 1.048
29 CPA C CPA N N N 0 -2.405 -0.981 2.45
30 CP7 C CP7 R N N 0 -3.677 -0.972 3.3
31 CP9 C CP9 N N N 0 -1.351 -0.083 3.1
32 CP8 C CP8 N N N 0 -1.868 -2.41 2.351
33 OP3 O OP3 N N N 0 -4.7 -1.716 2.636
34 CP6 C CP6 N N N 0 -3.39 -1.599 4.64
35 OP2 O OP2 N N N 0 -3.799 -2.713 4.889
36 NP2 N NP2 N N N 0 -2.678 -0.921 5.563
37 CP5 C CP5 N N N 0 -2.382 -1.538 6.858
38 CP4 C CP4 N N N 0 -1.568 -0.565 7.712
39 CP3 C CP3 N N N 0 -1.263 -1.2 9.045
40 OP1 O OP1 N N N 0 -1.658 -2.32 9.287
41 NP1 N NP1 N N N 0 -0.551 -0.522 9.967
42 CP2 C CP2 N N N 0 -0.255 -1.139 11.262
43 CP1 C CP1 N N N 0 0.558 -0.166 12.117
44 S S S N N N 0 0.924 -0.928 13.717
45 P3 P P3 N N N 0 -0.18 4.165 -8.765
46 O31 O O31 N N N 0 0.516 5.559 -9.17
47 O32 O O32 N N N 0 -1.174 3.7 -9.943
48 O33 O O33 N N N 0 -0.949 4.345 -7.513
49 CM1 C CM1 N N N 0 1.816 0.334 14.452
50 CM2 C CM2 N N N 0 2.356 0.162 15.848
51 CM3 C CM3 N N N 0 3.108 1.428 16.263
52 OM2 O OM2 N N N 0 2.012 1.368 13.848
53 CM4 C CM4 N N N 0 3.656 1.254 17.681
54 CM5 C CM5 N N N 0 4.408 2.52 18.096
55 CM6 C CM6 N N N 0 4.957 2.345 19.514
56 H2 H H2 N N N 0 4.928 -1.693 -12.212
57 H8 H H8 N N N 0 0.306 -2.435 -7.687
58 HN61 H 1HN6 N N N 0 3.301 -5.931 -11.773
59 HN62 H 2HN6 N N N 0 2.139 -5.859 -10.562
60 H1' H H1' N N N 0 2.688 0.426 -8.588
61 H2' H H2' N N N 0 -0.259 0.07 -9.371
62 HO2 H HO2 N N N 0 1.368 0.504 -10.974
63 H3' H H3' N N N 0 -0.802 2.004 -8.144
64 H4' H H4' N N N 0 1.578 1.945 -6.458
65 H5'1 H 1H5' N N N 0 -1.138 0.568 -6.214
66 H5'2 H 2H5' N N N 0 -0.77 2.226 -5.681
67 H12 H H12 N N N 0 -1.01 2.703 -3.034
68 H22 H H22 N N N 0 -1.824 2.123 -0.668
69 HPB1 H 1HPB N N N 0 -3.477 -1.098 0.585
70 HPB2 H 2HPB N N N 0 -3.109 0.559 1.118
71 HP7 H HP7 N N N 0 -4.011 0.055 3.444
72 HP91 H 1HP9 N N N 0 -1.779 0.901 3.29
73 HP92 H 2HP9 N N N 0 -1.027 -0.526 4.041
74 HP93 H 3HP9 N N N 0 -0.496 0.015 2.431
75 HP81 H 1HP8 N N N 0 -2.619 -3.049 1.888
76 HP82 H 2HP8 N N N 0 -0.962 -2.416 1.745
77 HP83 H 3HP8 N N N 0 -1.64 -2.782 3.35
78 HP3 H HP3 N N N 0 -4.365 -2.617 2.528
79 HP2 H HP2 N N N 0 -2.362 -0.025 5.369
80 HP51 H 1HP5 N N N 0 -1.809 -2.452 6.702
81 HP52 H 2HP5 N N N 0 -3.315 -1.777 7.368
82 HP41 H 1HP4 N N N 0 -2.141 0.348 7.868
83 HP42 H 2HP4 N N N 0 -0.635 -0.326 7.202
84 HP1 H HP1 N N N 0 -0.235 0.373 9.773
85 HP21 H 1HP2 N N N 0 0.317 -2.053 11.107
86 HP22 H 2HP2 N N N 0 -1.188 -1.378 11.773
87 HP11 H 1HP1 N N N 0 -0.014 0.747 12.272
88 HP12 H 2HP1 N N N 0 1.491 0.072 11.606
89 H31 H H31 N N N 0 -0.195 6.202 -9.294
90 H32 H H32 N N N 0 -0.635 3.595 -10.738
91 HM21 H 1HM2 N N N 0 3.037 -0.688 15.872
92 HM22 H 2HM2 N N N 0 1.531 -0.012 16.538
93 HM31 H 1HM3 N N N 0 2.427 2.279 16.24
94 HM32 H 2HM3 N N N 0 3.933 1.604 15.573
95 HM41 H 1HM4 N N N 0 4.337 0.403 17.705
96 HM42 H 2HM4 N N N 0 2.831 1.078 18.371
97 HM51 H 1HM5 N N N 0 3.727 3.371 18.073
98 HM52 H 2HM5 N N N 0 5.233 2.696 17.406
99 HM61 H 1HM6 N N N 0 5.492 3.247 19.81
100 HM62 H 2HM6 N N N 0 4.131 2.17 20.204
101 HM63 H 3HM6 N N N 0 5.637 1.494 19.538



HXC : Chemical Bonds

Total Number of Bonds: 103
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C2 N3 C N doub 1.32 N Y
2 C2 N1 C N sing 1.32 N Y
3 C2 H2 C H sing 1.08 N N
4 C4 C5 C C doub 1.41 N Y
5 C4 N9 C N sing 1.37 N Y
6 C4 N3 C N sing 1.33 N Y
7 C5 C6 C C sing 1.41 N Y
8 C5 N7 C N sing 1.35 N Y
9 C6 N1 C N doub 1.33 N Y
10 C6 N6 C N sing 1.38 N N
11 C8 N9 C N sing 1.36 N Y
12 C8 N7 C N doub 1.3 N Y
13 C8 H8 C H sing 1.08 N N
14 N9 C1' N C sing 1.46 N N
15 N6 HN61 N H sing 0.97 N N
16 N6 HN62 N H sing 0.97 N N
17 C1' C2' C C sing 1.55 N N
18 C1' O4' C O sing 1.44 N N
19 C1' H1' C H sing 1.09 N N
20 C2' O2' C O sing 1.43 N N
21 C2' C3' C C sing 1.55 N N
22 C2' H2' C H sing 1.09 N N
23 O2' HO2 O H sing 0.97 N N
24 C3' O3' C O sing 1.43 N N
25 C3' C4' C C sing 1.54 N N
26 C3' H3' C H sing 1.09 N N
27 O3' P3 O P sing 1.61 N N
28 C4' O4' C O sing 1.44 N N
29 C4' C5' C C sing 1.53 N N
30 C4' H4' C H sing 1.09 N N
31 C5' O5' C O sing 1.43 N N
32 C5' H5'1 C H sing 1.09 N N
33 C5' H5'2 C H sing 1.09 N N
34 O5' P1 O P sing 1.61 N N
35 P1 O11 P O doub 1.48 N N
36 P1 O12 P O sing 1.61 N N
37 P1 O6 P O sing 1.61 N N
38 O12 H12 O H sing 0.97 N N
39 O6 P2 O P sing 1.61 N N
40 P2 O21 P O doub 1.48 N N
41 P2 O22 P O sing 1.61 N N
42 P2 O7 P O sing 1.61 N N
43 O22 H22 O H sing 0.97 N N
44 O7 CPB O C sing 1.43 N N
45 CPB CPA C C sing 1.53 N N
46 CPB HPB1 C H sing 1.09 N N
47 CPB HPB2 C H sing 1.09 N N
48 CPA CP7 C C sing 1.53 N N
49 CPA CP9 C C sing 1.53 N N
50 CPA CP8 C C sing 1.53 N N
51 CP7 OP3 C O sing 1.43 N N
52 CP7 CP6 C C sing 1.51 N N
53 CP7 HP7 C H sing 1.09 N N
54 CP9 HP91 C H sing 1.09 N N
55 CP9 HP92 C H sing 1.09 N N
56 CP9 HP93 C H sing 1.09 N N
57 CP8 HP81 C H sing 1.09 N N
58 CP8 HP82 C H sing 1.09 N N
59 CP8 HP83 C H sing 1.09 N N
60 OP3 HP3 O H sing 0.97 N N
61 CP6 OP2 C O doub 1.21 N N
62 CP6 NP2 C N sing 1.35 N N
63 NP2 CP5 N C sing 1.46 N N
64 NP2 HP2 N H sing 0.97 N N
65 CP5 CP4 C C sing 1.53 N N
66 CP5 HP51 C H sing 1.09 N N
67 CP5 HP52 C H sing 1.09 N N
68 CP4 CP3 C C sing 1.51 N N
69 CP4 HP41 C H sing 1.09 N N
70 CP4 HP42 C H sing 1.09 N N
71 CP3 OP1 C O doub 1.21 N N
72 CP3 NP1 C N sing 1.35 N N
73 NP1 CP2 N C sing 1.46 N N
74 NP1 HP1 N H sing 0.97 N N
75 CP2 CP1 C C sing 1.53 N N
76 CP2 HP21 C H sing 1.09 N N
77 CP2 HP22 C H sing 1.09 N N
78 CP1 S C S sing 1.81 N N
79 CP1 HP11 C H sing 1.09 N N
80 CP1 HP12 C H sing 1.09 N N
81 S CM1 S C sing 1.71 N N
82 P3 O31 P O sing 1.61 N N
83 P3 O32 P O sing 1.61 N N
84 P3 O33 P O doub 1.48 N N
85 O31 H31 O H sing 0.97 N N
86 O32 H32 O H sing 0.97 N N
87 CM1 CM2 C C sing 1.51 N N
88 CM1 OM2 C O doub 1.21 N N
89 CM2 CM3 C C sing 1.53 N N
90 CM2 HM21 C H sing 1.09 N N
91 CM2 HM22 C H sing 1.09 N N
92 CM3 CM4 C C sing 1.53 N N
93 CM3 HM31 C H sing 1.09 N N
94 CM3 HM32 C H sing 1.09 N N
95 CM4 CM5 C C sing 1.53 N N
96 CM4 HM41 C H sing 1.09 N N
97 CM4 HM42 C H sing 1.09 N N
98 CM5 CM6 C C sing 1.53 N N
99 CM5 HM51 C H sing 1.09 N N
100 CM5 HM52 C H sing 1.09 N N
101 CM6 HM61 C H sing 1.09 N N
102 CM6 HM62 C H sing 1.09 N N
103 CM6 HM63 C H sing 1.09 N N



HXC : Used in PDB Entries

Total Number of PDB Entries: 10
Ligand Code PDB Entry ID Type Total Distinct
HXC 1chw Open in New Window Bound ligand 2 1
HXC 1mj3 Open in New Window Bound ligand 5 1
HXC 1w6u Open in New Window Bound ligand 4 1
HXC 1wn3 Open in New Window Bound ligand 4 1
HXC 3v1u Open in New Window Bound ligand 1 1
HXC 4fc6 Open in New Window Bound ligand 4 1
HXC 4rpm Open in New Window Bound ligand 1 1
HXC 5inf Open in New Window Bound ligand 1 1
HXC 5ini Open in New Window Bound ligand 4 1
HXC 5t06 Open in New Window Bound ligand 1 1