Chemical Components in the PDB

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MIA : Summary

Code

MIA

One-letter code

A

Molecule name

2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 12.01 N-(3-methylbut-2-en-1-yl)-2-(methylsulfanyl)adenosine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 2.0.7 [(2~{R},3~{S},4~{R},5~{R})-5-[6-(3-methylbut-2-enylamino)-2-methylsulfanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C16 H24 N5 O7 P S

Formal charge

0

Molecular weight

461.43 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OP(=O)(O)OCC1OC(C(C1O)O)n2cnc3c(NC\C=C(\C)C)nc(nc23)SC
SMILES CACTVS 3.385 CSc1nc(NCC=C(C)C)c2ncn([CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O)c2n1
SMILES OpenEye OEToolkits 2.0.7 CC(=CCNc1c2c(nc(n1)SC)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)C
Canonical SMILES CACTVS 3.385 CSc1nc(NCC=C(C)C)c2ncn([C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O)c2n1
Canonical SMILES OpenEye OEToolkits 2.0.7 CC(=CCNc1c2c(nc(n1)SC)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)C

IUPAC InChI

InChI=1S/C16H24N5O7PS/c1-8(2)4-5-17-13-10-14(20-16(19-13)30-3)21(7-18-10)15-12(23)11(22)9(28-15)6-27-29(24,25)26/h4,7,9,11-12,15,22-23H,5-6H2,1-3H3,(H,17,19,20)(H2,24,25,26)/t9-,11-,12-,15-/m1/s1

IUPAC InChI key

XBXAAXAANNIENQ-SDBHATRESA-N
MIA

wwPDB Information

Atom count

54 (30 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

A

Defined at

1999-07-08

Last modified at

2019-06-13

Status

Released

Obsoleted

Not Assigned



MIA : Atoms of Molecule

Total Number of Atoms: 54
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OP3 O O3P N N Y 0 6.51 -2.754 -1.685
2 P P P N N N 0 6.383 -1.827 -0.375
3 OP1 O O1P N N N 0 6.044 -2.668 0.794
4 OP2 O O2P N N N 0 7.783 -1.078 -0.109
5 O5' O O5' N N N 0 5.224 -0.733 -0.603
6 C5' C C5' N N N 0 4.797 0.173 0.417
7 C4' C C4' R N N 0 3.686 1.071 -0.131
8 O4' O O4' N N N 0 2.515 0.286 -0.409
9 C3' C C3' S N N 0 3.293 2.122 0.926
10 O3' O O3' N N N 0 3.511 3.442 0.424
11 C2' C C2' R N N 0 1.784 1.874 1.164
12 O2' O O2' N N N 0 1.076 3.111 1.28
13 C1' C C1' R N N 0 1.371 1.12 -0.126
14 N9 N N9 N Y N 0 0.181 0.3 0.114
15 C8 C C8 N Y N 0 0.167 -1.0 0.527
16 N7 N N7 N Y N 0 -1.061 -1.417 0.639
17 C5 C C5 N Y N 0 -1.91 -0.414 0.306
18 C6 C C6 N Y N 0 -3.309 -0.286 0.242
19 N1 N N1 N Y N 0 -3.824 0.878 -0.136
20 N6 N N6 N N N 0 -4.131 -1.35 0.567
21 C2 C C2 N Y N 0 -3.042 1.905 -0.449
22 N3 N N3 N Y N 0 -1.722 1.827 -0.403
23 C4 C C4 N Y N 0 -1.123 0.701 -0.029
24 S10 S S10 N N N 0 -3.788 3.423 -0.943
25 C11 C C11 N N N 0 -5.536 2.966 -0.827
26 C12 C C12 N N N 0 -5.587 -1.2 0.495
27 C13 C C13 N N N 0 -6.246 -2.494 0.896
28 C14 C C14 N N N 0 -7.088 -3.08 0.081
29 C15 C C15 N N N 0 -7.505 -2.393 -1.194
30 C16 C C16 N N N 0 -7.639 -4.441 0.418
31 HOP3 H HOP3 N N Y 0 7.191 -3.438 -1.618
32 HOP2 H HOP2 N N N 0 8.068 -0.507 -0.836
33 H5' H H5'1 N N N 0 4.42 -0.392 1.27
34 H5'' H H5'2 N N N 0 5.64 0.788 0.733
35 H4' H H4' N N N 0 4.025 1.566 -1.041
36 H3' H H3' N N N 0 3.857 1.967 1.846
37 HO3' H H3T N N Y 0 3.28 4.143 1.048
38 H2' H H2' N N N 0 1.625 1.253 2.046
39 HO2' H HO'2 N N N 0 1.364 3.66 2.022
40 H1' H H1' N N N 0 1.197 1.822 -0.942
41 H8 H H8 N N N 0 1.044 -1.596 0.73
42 HN6 H HN6 N N N 0 -3.744 -2.196 0.842
43 H111 H H111 N N N 0 -5.767 2.672 0.196
44 H112 H H112 N N N 0 -6.154 3.819 -1.108
45 H113 H H113 N N N 0 -5.739 2.133 -1.5
46 H121 H H121 N N N 0 -5.904 -0.406 1.171
47 H122 H H122 N N N 0 -5.876 -0.945 -0.525
48 H131 H H131 N N N 0 -6.024 -2.939 1.855
49 H151 H H151 N N N 0 -6.771 -2.597 -1.974
50 H152 H H152 N N N 0 -8.48 -2.766 -1.506
51 H153 H H153 N N N 0 -7.565 -1.318 -1.025
52 H161 H H161 N N N 0 -8.18 -4.39 1.363
53 H162 H H162 N N N 0 -8.318 -4.764 -0.371
54 H163 H H163 N N N 0 -6.819 -5.154 0.507



MIA : Chemical Bonds

Total Number of Bonds: 56
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OP3 P O P sing 1.61 N N
2 OP3 HOP3 O H sing 0.97 N N
3 P OP1 P O doub 1.48 N N
4 P OP2 P O sing 1.61 N N
5 P O5' P O sing 1.61 N N
6 OP2 HOP2 O H sing 0.97 N N
7 O5' C5' O C sing 1.43 N N
8 C5' C4' C C sing 1.53 N N
9 C5' H5' C H sing 1.09 N N
10 C5' H5'' C H sing 1.09 N N
11 C4' O4' C O sing 1.44 N N
12 C4' C3' C C sing 1.54 N N
13 C4' H4' C H sing 1.09 N N
14 O4' C1' O C sing 1.44 N N
15 C3' O3' C O sing 1.43 N N
16 C3' C2' C C sing 1.55 N N
17 C3' H3' C H sing 1.09 N N
18 O3' HO3' O H sing 0.97 N N
19 C2' O2' C O sing 1.43 N N
20 C2' C1' C C sing 1.55 N N
21 C2' H2' C H sing 1.09 N N
22 O2' HO2' O H sing 0.97 N N
23 C1' N9 C N sing 1.46 N N
24 C1' H1' C H sing 1.09 N N
25 N9 C8 N C sing 1.36 N Y
26 N9 C4 N C sing 1.37 N Y
27 C8 N7 C N doub 1.3 N Y
28 C8 H8 C H sing 1.08 N N
29 N7 C5 N C sing 1.36 N Y
30 C5 C6 C C sing 1.41 N Y
31 C5 C4 C C doub 1.41 N Y
32 C6 N6 C N sing 1.38 N N
33 C6 N1 C N doub 1.33 N Y
34 N6 C12 N C sing 1.47 N N
35 N6 HN6 N H sing 0.97 N N
36 N1 C2 N C sing 1.33 N Y
37 C2 N3 C N doub 1.32 N Y
38 C2 S10 C S sing 1.76 N N
39 N3 C4 N C sing 1.33 N Y
40 S10 C11 S C sing 1.81 N N
41 C11 H111 C H sing 1.09 N N
42 C11 H112 C H sing 1.09 N N
43 C11 H113 C H sing 1.09 N N
44 C12 C13 C C sing 1.51 N N
45 C12 H121 C H sing 1.09 N N
46 C12 H122 C H sing 1.09 N N
47 C13 C14 C C doub 1.31 N N
48 C13 H131 C H sing 1.08 N N
49 C14 C15 C C sing 1.51 N N
50 C14 C16 C C sing 1.51 N N
51 C15 H151 C H sing 1.09 N N
52 C15 H152 C H sing 1.09 N N
53 C15 H153 C H sing 1.09 N N
54 C16 H161 C H sing 1.09 N N
55 C16 H162 C H sing 1.09 N N
56 C16 H163 C H sing 1.09 N N



MIA : Used in PDB Entries

Total Number of PDB Entries: 160
Ligand Code PDB Entry ID Type Total Distinct
MIA 1b23 Open in New Window Polymer component 1 1
MIA 1vy4 Open in New Window Polymer component 4 2
MIA 1vy5 Open in New Window Polymer component 4 2
MIA 1vy7 Open in New Window Polymer component 2 1
MIA 3bbv Open in New Window Polymer component 1 1
MIA 3j46 Open in New Window Polymer component 1 1
MIA 4cxg Open in New Window Polymer component 1 1
MIA 4cxh Open in New Window Polymer component 1 1
MIA 4uje Open in New Window Polymer component 1 1
MIA 4v4i Open in New Window Polymer component 1 1
MIA 4v5l Open in New Window Polymer component 1 1
MIA 4v5p Open in New Window Polymer component 2 1
MIA 4v5q Open in New Window Polymer component 2 1
MIA 4v5r Open in New Window Polymer component 2 1
MIA 4v5s Open in New Window Polymer component 2 1
MIA 4v6f Open in New Window Polymer component 6 1
MIA 4v6k Open in New Window Polymer component 2 1
MIA 4v6l Open in New Window Polymer component 2 1
MIA 4v6n Open in New Window Polymer component 1 1
MIA 4v6o Open in New Window Polymer component 1 1
MIA 4v6p Open in New Window Polymer component 1 1
MIA 4v6q Open in New Window Polymer component 1 1
MIA 4v6r Open in New Window Polymer component 1 1
MIA 4v8d Open in New Window Polymer component 4 1
MIA 4v8e Open in New Window Polymer component 4 1
MIA 4v8f Open in New Window Polymer component 4 1
MIA 4w2e Open in New Window Polymer component 2 1
MIA 4w2f Open in New Window Polymer component 4 1
MIA 4w2g Open in New Window Polymer component 4 1
MIA 4w2h Open in New Window Polymer component 2 1
MIA 4w2i Open in New Window Polymer component 4 1
MIA 4wpo Open in New Window Polymer component 4 2
MIA 4wq1 Open in New Window Polymer component 4 1
MIA 4wqf Open in New Window Polymer component 4 1
MIA 4wqr Open in New Window Polymer component 2 1
MIA 4wqu Open in New Window Polymer component 4 1
MIA 4wr6 Open in New Window Polymer component 2 1
MIA 4wra Open in New Window Polymer component 2 2
MIA 4wro Open in New Window Polymer component 4 2
MIA 4wsd Open in New Window Polymer component 3 3
MIA 4wt1 Open in New Window Polymer component 1 1
MIA 4wu1 Open in New Window Polymer component 4 1
MIA 4wzd Open in New Window Polymer component 4 1
MIA 4wzo Open in New Window Polymer component 2 1
MIA 4y4p Open in New Window Polymer component 4 1
MIA 4z3s Open in New Window Polymer component 4 1
MIA 5afi Open in New Window Polymer component 1 1
MIA 5doy Open in New Window Polymer component 4 1
MIA 5j4b Open in New Window Polymer component 4 1
MIA 5j4c Open in New Window Polymer component 4 1
MIA 5j8b Open in New Window Polymer component 2 2
MIA 5vp2 Open in New Window Polymer component 4 1
MIA 5w4k Open in New Window Polymer component 2 1
MIA 5wdt Open in New Window Polymer component 1 1
MIA 5we4 Open in New Window Polymer component 1 1
MIA 5we6 Open in New Window Polymer component 1 1
MIA 5wf0 Open in New Window Polymer component 1 1
MIA 5wfk Open in New Window Polymer component 1 1
MIA 5wfs Open in New Window Polymer component 1 1
MIA 5wis Open in New Window Polymer component 4 1
MIA 5wit Open in New Window Polymer component 4 2
MIA 6az1 Open in New Window Polymer component 1 1
MIA 6cfj Open in New Window Polymer component 4 1
MIA 6n1d Open in New Window Polymer component 1 1
MIA 6nd5 Open in New Window Polymer component 4 1
MIA 6qnr Open in New Window Polymer component 7 6
MIA 6ucq Open in New Window Polymer component 4 1
MIA 6uo1 Open in New Window Polymer component 4 1
MIA 6xhv Open in New Window Polymer component 4 2
MIA 6xhw Open in New Window Polymer component 4 2
MIA 6xhy Open in New Window Polymer component 4 2
MIA 6ysr Open in New Window Polymer component 1 1
MIA 6yss Open in New Window Polymer component 1 1
MIA 6yst Open in New Window Polymer component 1 1
MIA 6ysu Open in New Window Polymer component 1 1
MIA 6zj3 Open in New Window Polymer component 1 1
MIA 6ztj Open in New Window Polymer component 1 1
MIA 6ztl Open in New Window Polymer component 1 1
MIA 6ztm Open in New Window Polymer component 1 1
MIA 6ztn Open in New Window Polymer component 2 1
MIA 6zto Open in New Window Polymer component 1 1
MIA 6ztp Open in New Window Polymer component 1 1
MIA 6zu1 Open in New Window Polymer component 1 1
MIA 7abz Open in New Window Polymer component 1 1
MIA 7ac7 Open in New Window Polymer component 1 1
MIA 7azo Open in New Window Polymer component 7 5
MIA 7azs Open in New Window Polymer component 7 5
MIA 7n1p Open in New Window Polymer component 1 1
MIA 7n2c Open in New Window Polymer component 1 1
MIA 7n2u Open in New Window Polymer component 1 1
MIA 7n2v Open in New Window Polymer component 1 1
MIA 7n30 Open in New Window Polymer component 1 1
MIA 7n31 Open in New Window Polymer component 1 1
MIA 7pjs Open in New Window Polymer component 1 1
MIA 7pjt Open in New Window Polymer component 1 1
MIA 7pju Open in New Window Polymer component 1 1
MIA 7pjv Open in New Window Polymer component 1 1
MIA 7pjw Open in New Window Polymer component 1 1
MIA 7pjx Open in New Window Polymer component 1 1
MIA 7pjy Open in New Window Polymer component 1 1
MIA 7pjz Open in New Window Polymer component 1 1
MIA 7rq8 Open in New Window Polymer component 4 2
MIA 7rq9 Open in New Window Polymer component 4 2
MIA 7ug7 Open in New Window Polymer component 1 1
MIA 7zta Open in New Window Polymer component 1 1
MIA 8cvj Open in New Window Polymer component 4 2
MIA 8cvk Open in New Window Polymer component 4 2
MIA 8cvl Open in New Window Polymer component 4 2
MIA 8ekc Open in New Window Polymer component 1 1
MIA 8ev6 Open in New Window Polymer component 4 1
MIA 8ev7 Open in New Window Polymer component 4 1
MIA 8fzd Open in New Window Polymer component 1 1
MIA 8fze Open in New Window Polymer component 2 1
MIA 8fzf Open in New Window Polymer component 1 1
MIA 8fzg Open in New Window Polymer component 2 1
MIA 8fzh Open in New Window Polymer component 2 1
MIA 8fzi Open in New Window Polymer component 1 1
MIA 8fzj Open in New Window Polymer component 1 1
MIA 8g29 Open in New Window Polymer component 4 2
MIA 8g2a Open in New Window Polymer component 4 2
MIA 8g2b Open in New Window Polymer component 4 1
MIA 8g2c Open in New Window Polymer component 4 2
MIA 8g2d Open in New Window Polymer component 4 1
MIA 8g5z Open in New Window Polymer component 1 1
MIA 8g60 Open in New Window Polymer component 1 1
MIA 8g6j Open in New Window Polymer component 1 1
MIA 8ifb Open in New Window Polymer component 1 1
MIA 8ifc Open in New Window Polymer component 1 1
MIA 8ip8 Open in New Window Polymer component 1 1
MIA 8ip9 Open in New Window Polymer component 1 1
MIA 8ipa Open in New Window Polymer component 1 1
MIA 8ipb Open in New Window Polymer component 1 1
MIA 8oin Open in New Window Polymer component 1 1
MIA 8oiq Open in New Window Polymer component 1 1
MIA 8peg Open in New Window Polymer component 1 1
MIA 8pkl Open in New Window Polymer component 1 1
MIA 8r3v Open in New Window Polymer component 2 2
MIA 8r6c Open in New Window Polymer component 1 1
MIA 8r8m Open in New Window Polymer component 1 1
MIA 8rcl Open in New Window Polymer component 2 2
MIA 8rcm Open in New Window Polymer component 2 2
MIA 8rcs Open in New Window Polymer component 2 2
MIA 8rct Open in New Window Polymer component 2 2
MIA 8rxh Open in New Window Polymer component 1 1
MIA 8rxx Open in New Window Polymer component 1 1
MIA 8syl Open in New Window Polymer component 2 1
MIA 8ud6 Open in New Window Polymer component 4 1
MIA 8ud7 Open in New Window Polymer component 4 1
MIA 8ud8 Open in New Window Polymer component 4 1
MIA 8uu5 Open in New Window Polymer component 1 1
MIA 8uu6 Open in New Window Polymer component 1 1
MIA 8uu7 Open in New Window Polymer component 1 1
MIA 8uu8 Open in New Window Polymer component 1 1
MIA 8uu9 Open in New Window Polymer component 1 1
MIA 8uvr Open in New Window Polymer component 4 1
MIA 8uvs Open in New Window Polymer component 4 1
MIA 8vtu Open in New Window Polymer component 4 2
MIA 8vtv Open in New Window Polymer component 4 2
MIA 8vtx Open in New Window Polymer component 4 2
MIA 9b00 Open in New Window Polymer component 4 1