Chemical Components in the PDB

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LYX : Summary

Code

LYX

One-letter code

K

Molecule name

N''-(2-COENZYME A)-PROPANOYL-LYSINE

Systematic names

ProgramVersionName
ACDLabs 10.04 (3S,5R,9R,19S,26S)-26-amino-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8,19-trimethyl-10,14,20-trioxo-2,4,6-trioxa-18-thia-11,15,21-triaza-3,5-diphosphaheptacosan-27-oic acid 3,5-dioxide (non-preferred name)
OpenEye OEToolkits 1.5.0 (2S)-2-amino-6-[[(2S)-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]propanoyl]amino]hexanoic acid

Formula

C30 H52 N9 O19 P3 S

Formal charge

0

Molecular weight

967.769 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(N)CCCCNC(=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)C
SMILES CACTVS 3.341 C[CH](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)C(=O)NCCCC[CH](N)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 CC(C(=O)NCCCCC(C(=O)O)N)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 C[C@H](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)C(=O)NCCCC[C@H](N)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C[C@@H](C(=O)NCCCC[C@@H](C(=O)O)N)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/C30H52N9O19P3S/c1-16(26(43)34-8-5-4-6-17(31)29(45)46)62-11-10-33-19(40)7-9-35-27(44)23(42)30(2,3)13-55-61(52,53)58-60(50,51)54-12-18-22(57-59(47,48)49)21(41)28(56-18)39-15-38-20-24(32)36-14-37-25(20)39/h14-18,21-23,28,41-42H,4-13,31H2,1-3H3,(H,33,40)(H,34,43)(H,35,44)(H,45,46)(H,50,51)(H,52,53)(H2,32,36,37)(H2,47,48,49)/t16-,17-,18+,21+,22+,23-,28+/m0/s1

IUPAC InChI key

RFJAZFUCRKBHCW-NFOKXICTSA-N
LYX

wwPDB Information

Atom count

114 (62 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

LYS

Defined at

2002-07-22

Last modified at

2024-09-27

Status

Released

Obsoleted

Not Assigned



LYX : Atoms of Molecule

Total Number of Atoms: 114
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O1 O O1 N N N 0 2.094 -6.645 -0.476
2 P2 P P2 S N N 0 1.834 -5.506 -1.419
3 O3 O O3 N N N 0 1.514 -4.1 -0.688
4 P4 P P4 R N N 0 2.395 -3.212 0.336
5 O5 O O5 N N N 0 1.365 -2.049 0.777
6 C6 C C6 N N N 0 0.101 -2.432 1.307
7 C7 C C7 N N N 0 -0.749 -1.191 1.673
8 C8 C C8 N N N 0 0.006 -0.369 2.745
9 C9 C C9 N N N 0 -0.918 -0.291 0.433
10 C10 C C10 R N N 0 -2.133 -1.609 2.253
11 O11 O O11 N N N 0 -2.89 -0.444 2.574
12 C12 C C12 N N N 0 -2.992 -2.432 1.296
13 N13 N N13 N N N 0 -2.815 -3.797 1.456
14 C14 C C14 N N N 0 -3.5 -4.779 0.648
15 C15 C C15 N N N 0 -2.669 -5.101 -0.587
16 C16 C C16 N N N 0 -3.341 -6.119 -1.49
17 N17 N N17 N N N 0 -2.568 -6.398 -2.608
18 C18 C C18 N N N 0 -2.975 -7.335 -3.629
19 C19 C C19 N N N 0 -2.507 -8.758 -3.352
20 S20 S S20 N N N 0 -0.694 -8.885 -3.29
21 C21 C C21 S N N 0 -0.57 -10.656 -2.955
22 C22 C C22 N N N 0 0.895 -11.067 -2.895
23 C23 C C23 N N N 0 -1.286 -10.933 -1.641
24 NZ N NZ N N N 0 -2.643 -11.167 -1.815
25 CE C CE N N N 0 -3.535 -11.434 -0.711
26 CD C CD N N N 0 -3.632 -12.93 -0.404
27 N N N N N N 0 -4.009 -15.991 -3.581
28 CG C CG N N N 0 -4.192 -13.746 -1.575
29 CB C CB N N N 0 -4.347 -15.238 -1.254
30 CA C CA S N N 0 -4.852 -16.092 -2.418
31 C C C N N N 0 -6.232 -15.63 -2.845
32 O O O N N N 0 -6.512 -15.157 -3.939
33 O33 O O33 N N N 0 -0.708 -10.928 -0.556
34 O34 O O34 N N N 0 -4.433 -6.622 -1.241
35 O35 O O35 N N N 0 -3.736 -1.911 0.467
36 O36 O O36 N N N 0 3.711 -2.746 -0.215
37 O37 O O37 N N N 0 2.498 -4.159 1.643
38 O38 O O38 N N N 0 0.556 -5.719 -2.387
39 O39 O O39 N N N 0 3.053 -5.17 -2.429
40 C40 C C40 N N N 0 2.927 -4.115 -3.366
41 C41 C C41 R N N 0 4.205 -4.019 -4.179
42 C42 C C42 S N N 0 4.175 -2.922 -5.229
43 O43 O O43 N N N 0 4.458 -1.653 -4.68
44 P44 P P44 N N N 0 4.579 -0.397 -5.686
45 O45 O O45 N N N 0 5.652 -0.516 -6.729
46 O46 O O46 N N N 0 4.712 0.878 -4.7
47 O47 O O47 N N N 0 3.075 -0.264 -6.266
48 C48 C C48 R N N 0 5.218 -3.397 -6.222
49 O49 O O49 N N N 0 6.53 -3.01 -5.818
50 C50 C C50 R N N 0 5.095 -4.92 -6.142
51 N51 N N51 N Y N 0 4.376 -5.51 -7.272
52 C52 C C52 N Y N 0 4.94 -6.005 -8.419
53 N53 N N53 N Y N 0 4.037 -6.472 -9.256
54 C54 C C54 N Y N 0 2.835 -6.271 -8.625
55 C55 C C55 N Y N 0 3.024 -5.674 -7.389
56 N56 N N56 N Y N 0 2.079 -5.332 -6.5
57 C57 C C57 N Y N 0 0.853 -5.652 -6.967
58 N58 N N58 N Y N 0 0.517 -6.233 -8.144
59 C59 C C59 N Y N 0 1.523 -6.551 -8.994
60 N60 N N60 N N N 0 1.239 -7.156 -10.231
61 O61 O O61 N N N 0 4.407 -5.238 -4.914
62 OXT O OXT N N Y 0 -7.141 -15.752 -1.841
63 H61 H 1H6 N N N 0 -0.401 -3.042 0.549
64 H62 H 2H6 N N N 0 0.283 -3.059 2.187
65 H81 H 1H8 N N N 0 -0.59 0.492 3.07
66 H82 H 2H8 N N N 0 0.957 0.019 2.362
67 H83 H 3H8 N N N 0 0.231 -0.973 3.63
68 H91 H 1H9 N N N 0 0.042 0.125 0.105
69 H92 H 2H9 N N N 0 -1.583 0.554 0.647
70 H93 H 3H9 N N N 0 -1.334 -0.846 -0.414
71 H10 H H10 N N N 0 -1.993 -2.169 3.186
72 H11 H H11 N N N 0 -3.268 -0.123 1.742
73 H13 H H13 N N N 0 -2.157 -4.137 2.15
74 H141 H 1H14 N N N 0 -3.67 -5.683 1.243
75 H142 H 2H14 N N N 0 -4.482 -4.39 0.359
76 H151 H 1H15 N N N 0 -1.69 -5.497 -0.288
77 H152 H 2H15 N N N 0 -2.49 -4.188 -1.168
78 H17 H H17 N N N 0 -1.677 -5.922 -2.714
79 H181 H 1H18 N N N 0 -4.07 -7.312 -3.655
80 H182 H 2H18 N N N 0 -2.61 -6.965 -4.593
81 H191 H 1H19 N N N 0 -2.913 -9.124 -2.403
82 H192 H 2H19 N N N 0 -2.859 -9.42 -4.149
83 H211 H 1H21 N N N 0 -1.063 -11.2 -3.768
84 H221 H 1H22 N N N 0 1.445 -10.532 -2.112
85 H222 H 2H22 N N N 0 0.98 -12.137 -2.671
86 H223 H 3H22 N N N 0 1.398 -10.89 -3.852
87 HZ H HZ N N N 0 -3.045 -11.107 -2.745
88 HE3 H 1HE N N N 0 -4.528 -11.034 -0.944
89 HE2 H 2HE N N N 0 -3.171 -10.908 0.178
90 HD3 H 1HD N N N 0 -2.642 -13.305 -0.121
91 HD2 H 2HD N N N 0 -4.283 -13.062 0.47
92 HG3 H 1HG N N N 0 -5.18 -13.353 -1.842
93 HG2 H 2HG N N N 0 -3.557 -13.623 -2.46
94 HB3 H 1HB N N N 0 -5.038 -15.333 -0.405
95 HB2 H 2HB N N N 0 -3.384 -15.629 -0.903
96 HA H HA N N N 0 -4.896 -17.155 -2.163
97 H H H N N N 0 -4.436 -15.883 -4.486
98 H2 H HN2 N N Y 0 -3.035 -16.231 -3.502
99 H37 H H37 N N N 0 3.069 -3.878 2.39
100 H38 H H38 N N N 0 0.446 -6.58 -2.845
101 H401 H 1H40 N N N 0 2.072 -4.322 -4.018
102 H402 H 2H40 N N N 0 2.746 -3.181 -2.825
103 H41 H H41 N N N 0 5.049 -3.888 -3.492
104 H42 H H42 N N N 0 3.193 -2.889 -5.716
105 H46 H H46 N N N 0 4.863 1.765 -5.09
106 H47 H H47 N N N 0 2.898 0.382 -6.983
107 H48 H H48 N N N 0 5.061 -2.99 -7.226
108 H49 H H49 N N N 0 6.646 -3.3 -4.896
109 H50 H H50 N N N 0 6.069 -5.42 -6.129
110 H52 H H52 N N N 0 6.008 -5.997 -8.586
111 H57 H H57 N N N 0 0.023 -5.409 -6.312
112 H601 H 1H60 N N N 0 1.43 -6.657 -11.079
113 H602 H 2H60 N N N 0 0.763 -8.038 -10.25
114 HXT H HXT N N Y 0 -8.044 -15.433 -2.054



LYX : Chemical Bonds

Total Number of Bonds: 116
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1 P2 O P doub 1.5 N N
2 P2 O3 P O sing 1.62 N N
3 P2 O38 P O sing 1.62 N N
4 P2 O39 P O sing 1.62 N N
5 O3 P4 O P sing 1.62 N N
6 P4 O5 P O sing 1.61 N N
7 P4 O36 P O doub 1.5 N N
8 P4 O37 P O sing 1.62 N N
9 O5 C6 O C sing 1.42 N N
10 C6 C7 C C sing 1.55 N N
11 C6 H61 C H sing 1.09 N N
12 C6 H62 C H sing 1.1 N N
13 C7 C8 C C sing 1.55 N N
14 C7 C9 C C sing 1.54 N N
15 C7 C10 C C sing 1.56 N N
16 C8 H81 C H sing 1.1 N N
17 C8 H82 C H sing 1.1 N N
18 C8 H83 C H sing 1.09 N N
19 C9 H91 C H sing 1.1 N N
20 C9 H92 C H sing 1.1 N N
21 C9 H93 C H sing 1.09 N N
22 C10 O11 C O sing 1.43 N N
23 C10 C12 C C sing 1.53 N N
24 C10 H10 C H sing 1.1 N N
25 O11 H11 O H sing 0.97 N N
26 C12 N13 C N sing 1.39 N N
27 C12 O35 C O doub 1.23 N N
28 N13 C14 N C sing 1.44 N N
29 N13 H13 N H sing 1.01 N N
30 C14 C15 C C sing 1.52 N N
31 C14 H141 C H sing 1.1 N N
32 C14 H142 C H sing 1.1 N N
33 C15 C16 C C sing 1.52 N N
34 C15 H151 C H sing 1.1 N N
35 C15 H152 C H sing 1.1 N N
36 C16 N17 C N sing 1.39 N N
37 C16 O34 C O doub 1.23 N N
38 N17 C18 N C sing 1.44 N N
39 N17 H17 N H sing 1.02 N N
40 C18 C19 C C sing 1.52 N N
41 C18 H181 C H sing 1.1 N N
42 C18 H182 C H sing 1.1 N N
43 C19 S20 C S sing 1.82 N N
44 C19 H191 C H sing 1.1 N N
45 C19 H192 C H sing 1.09 N N
46 S20 C21 S C sing 1.81 N N
47 C21 C22 C C sing 1.52 N N
48 C21 C23 C C sing 1.52 N N
49 C21 H211 C H sing 1.1 N N
50 C22 H221 C H sing 1.1 N N
51 C22 H222 C H sing 1.1 N N
52 C22 H223 C H sing 1.1 N N
53 C23 NZ C N sing 1.39 N N
54 C23 O33 C O doub 1.23 N N
55 NZ CE N C sing 1.44 N N
56 NZ HZ N H sing 1.01 N N
57 CE CD C C sing 1.53 N N
58 CE HE3 C H sing 1.1 N N
59 CE HE2 C H sing 1.1 N N
60 CD CG C C sing 1.53 N N
61 CD HD3 C H sing 1.1 N N
62 CD HD2 C H sing 1.1 N N
63 CG CB C C sing 1.53 N N
64 CG HG3 C H sing 1.1 N N
65 CG HG2 C H sing 1.1 N N
66 CB CA C C sing 1.53 N N
67 CB HB3 C H sing 1.1 N N
68 CB HB2 C H sing 1.1 N N
69 CA N C N sing 1.44 N N
70 CA C C C sing 1.52 N N
71 CA HA C H sing 1.09 N N
72 N H N H sing 1.01 N N
73 N H2 N H sing 1.01 N N
74 C O C O doub 1.22 N N
75 C OXT C O sing 1.36 N N
76 O37 H37 O H sing 0.98 N N
77 O38 H38 O H sing 0.98 N N
78 O39 C40 O C sing 1.42 N N
79 C40 C41 C C sing 1.52 N N
80 C40 H401 C H sing 1.09 N N
81 C40 H402 C H sing 1.09 N N
82 C41 C42 C C sing 1.52 N N
83 C41 O61 C O sing 1.44 N N
84 C41 H41 C H sing 1.1 N N
85 C42 O43 C O sing 1.41 N N
86 C42 C48 C C sing 1.52 N N
87 C42 H42 C H sing 1.1 N N
88 O43 P44 O P sing 1.61 N N
89 P44 O45 P O doub 1.5 N N
90 P44 O46 P O sing 1.62 N N
91 P44 O47 P O sing 1.62 N N
92 O46 H46 O H sing 0.98 N N
93 O47 H47 O H sing 0.98 N N
94 C48 O49 C O sing 1.43 N N
95 C48 C50 C C sing 1.53 N N
96 C48 H48 C H sing 1.09 N N
97 O49 H49 O H sing 0.97 N N
98 C50 N51 C N sing 1.46 N N
99 C50 O61 C O sing 1.44 N N
100 C50 H50 C H sing 1.09 N N
101 N51 C52 N C sing 1.37 N Y
102 N51 C55 N C sing 1.37 N Y
103 C52 N53 C N doub 1.32 N Y
104 C52 H52 C H sing 1.08 N N
105 N53 C54 N C sing 1.37 N Y
106 C54 C55 C C doub 1.39 N Y
107 C54 C59 C C sing 1.39 N Y
108 C55 N56 C N sing 1.34 N Y
109 N56 C57 N C doub 1.35 N Y
110 C57 N58 C N sing 1.35 N Y
111 C57 H57 C H sing 1.08 N N
112 N58 C59 N C doub 1.35 N Y
113 C59 N60 C N sing 1.41 N N
114 N60 H601 N H sing 1.0 N N
115 N60 H602 N H sing 1.0 N N
116 OXT HXT O H sing 0.98 N N



LYX : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
LYX 1m1d Open in New Window Polymer component 2 1
LYX 2ekg Open in New Window Polymer component 2 1
LYX 3itg Open in New Window Polymer component 2 1