Chemical Components in the PDB

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KAA : Summary

Code

KAA

One-letter code

X

Molecule name

5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE

Synonyms

5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE

Systematic names

ProgramVersionName
ACDLabs 10.04 5'-O-(L-lysylsulfamoyl)adenosine
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl N-[(2S)-2,6-diaminohexanoyl]sulfamate

Formula

C16 H26 N8 O7 S

Formal charge

0

Molecular weight

474.492 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)CCCCN
SMILES CACTVS 3.341 NCCCC[CH](N)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
SMILES OpenEye OEToolkits 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)C(CCCCN)N)O)O)N
Canonical SMILES CACTVS 3.341 NCCCC[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
Canonical SMILES OpenEye OEToolkits 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)[C@H](CCCCN)N)O)O)N

IUPAC InChI

InChI=1S/C16H26N8O7S/c17-4-2-1-3-8(18)15(27)23-32(28,29)30-5-9-11(25)12(26)16(31-9)24-7-22-10-13(19)20-6-21-14(10)24/h6-9,11-12,16,25-26H,1-5,17-18H2,(H,23,27)(H2,19,20,21)/t8-,9+,11+,12+,16+/m0/s1

IUPAC InChI key

NARKTLKJPPMFJF-LEJQEAHTSA-N
KAA

wwPDB Information

Atom count

58 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2007-04-13

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



KAA : Atoms of Molecule

Total Number of Atoms: 58
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 NZ N NZ N N N 0 -2.763 5.667 7.546
2 CE C CE N N N 0 -2.073 5.375 6.295
3 CD C CD N N N 0 -2.331 6.483 5.276
4 CG C CG N N N 0 -1.607 6.2 3.957
5 CB C CB N N N 0 -1.894 7.292 2.919
6 CA C CA S N N 0 -1.158 7.045 1.596
7 N N N N N N 0 -1.479 8.09 0.623
8 C C C N N N 0 -1.585 5.728 0.969
9 O O O N N N 0 -2.688 5.224 1.155
10 N8 N N8 N N N 0 -0.585 5.136 0.13
11 S1 S S1 N N N 0 -0.781 3.654 -0.709
12 O1S O O1S N N N 0 0.127 3.669 -1.841
13 O2S O O2S N N N 0 -2.201 3.432 -0.913
14 O5' O O5* N N N 0 -0.238 2.541 0.36
15 C5' C C5* N N N 0 -0.881 2.428 1.621
16 C4' C C4* R N N 0 -0.199 1.333 2.429
17 O4' O O4* N N N 0 1.179 1.716 2.644
18 C3' C C3* S N N 0 -0.816 1.144 3.811
19 O3' O O3* N N N 0 -0.579 -0.197 4.241
20 C2' C C2* R N N 0 -0.001 2.098 4.662
21 O2' O O2* N N N 0 -0.013 1.764 6.035
22 C1' C C1* R N N 0 1.384 1.94 4.052
23 N9 N N9 N Y N 0 2.255 3.097 4.246
24 C8 C C8 N Y N 0 2.314 4.207 3.444
25 N7 N N7 N Y N 0 3.197 5.084 3.873
26 C5 C C5 N Y N 0 3.736 4.519 5.001
27 C4 C C4 N Y N 0 3.163 3.282 5.251
28 N3 N N3 N Y N 0 3.443 2.448 6.263
29 C2 C C2 N Y N 0 4.398 2.975 7.06
30 N1 N N1 N Y N 0 5.043 4.161 6.942
31 C6 C C6 N Y N 0 4.71 4.953 5.894
32 N6 N N6 N N N 0 5.344 6.195 5.717
33 HNZ1 H 1HNZ N N N 0 -2.477 5.178 8.367
34 HNZ2 H 2HNZ N N N 0 -3.616 6.183 7.504
35 HE1 H 1HE N N N 0 -2.429 4.415 5.907
36 HE2 H 2HE N N N 0 -0.998 5.28 6.487
37 HD1 H 1HD N N N 0 -1.992 7.446 5.678
38 HD2 H 2HD N N N 0 -3.409 6.572 5.089
39 HG1 H 1HG N N N 0 -0.529 6.136 4.144
40 HG2 H 2HG N N N 0 -1.927 5.228 3.564
41 HB1 H 1HB N N N 0 -2.975 7.325 2.732
42 HB2 H 2HB N N N 0 -1.613 8.267 3.337
43 HA H HA N N N 0 -0.074 7.054 1.759
44 HN1 H 1HN N N N 0 -2.437 8.33 0.497
45 HN2 H 2HN N N N 0 -0.766 8.37 -0.012
46 HN8 H HN8 N N N 0 0.308 5.633 0.024
47 H5'1 H 1H5* N N N 0 -0.81 3.389 2.14
48 H5'2 H 2H5* N N N 0 -1.935 2.186 1.458
49 H4' H H4* N N N 0 -0.198 0.404 1.85
50 H3' H H3* N N N 0 -1.893 1.322 3.856
51 HO3' H HO3* N N N 0 -0.576 -0.744 3.441
52 H2' H H2* N N N 0 -0.369 3.124 4.543
53 HO2' H HO2* N N N 0 0.47 2.465 6.507
54 H1' H H1* N N N 0 1.934 1.09 4.471
55 H8 H H8 N N N 0 1.691 4.319 2.567
56 H2 H H2 N N N 0 4.69 2.366 7.909
57 HN61 H 1HN6 N N N 0 5.438 6.573 4.794
58 HN62 H 2HN6 N N N 0 5.777 6.643 6.502



KAA : Chemical Bonds

Total Number of Bonds: 60
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 NZ CE N C sing 1.46 N N
2 NZ HNZ1 N H sing 1.0 N N
3 NZ HNZ2 N H sing 1.0 N N
4 CE CD C C sing 1.53 N N
5 CE HE1 C H sing 1.09 N N
6 CE HE2 C H sing 1.1 N N
7 CD CG C C sing 1.53 N N
8 CD HD1 C H sing 1.1 N N
9 CD HD2 C H sing 1.1 N N
10 CG CB C C sing 1.53 N N
11 CG HG1 C H sing 1.1 N N
12 CG HG2 C H sing 1.1 N N
13 CB CA C C sing 1.53 N N
14 CB HB1 C H sing 1.1 N N
15 CB HB2 C H sing 1.1 N N
16 CA C C C sing 1.52 N N
17 CA N C N sing 1.46 N N
18 CA HA C H sing 1.1 N N
19 N HN1 N H sing 1.0 N N
20 N HN2 N H sing 0.99 N N
21 C O C O doub 1.23 N N
22 C N8 C N sing 1.43 N N
23 N8 S1 N S sing 1.71 N N
24 N8 HN8 N H sing 1.03 N N
25 S1 O1S S O doub 1.45 N N
26 S1 O5' S O sing 1.64 N N
27 S1 O2S S O doub 1.45 N N
28 O5' C5' O C sing 1.42 N N
29 C5' C4' C C sing 1.52 N N
30 C5' H5'1 C H sing 1.09 N N
31 C5' H5'2 C H sing 1.09 N N
32 C4' O4' C O sing 1.45 N N
33 C4' C3' C C sing 1.53 N N
34 C4' H4' C H sing 1.09 N N
35 O4' C1' O C sing 1.44 N N
36 C3' C2' C C sing 1.52 N N
37 C3' O3' C O sing 1.43 N N
38 C3' H3' C H sing 1.09 N N
39 O3' HO3' O H sing 0.97 N N
40 C2' C1' C C sing 1.52 N N
41 C2' O2' C O sing 1.41 N N
42 C2' H2' C H sing 1.1 N N
43 O2' HO2' O H sing 0.97 N N
44 C1' N9 C N sing 1.46 N N
45 C1' H1' C H sing 1.1 N N
46 N9 C4 N C sing 1.37 N Y
47 N9 C8 N C sing 1.37 N Y
48 C8 N7 C N doub 1.32 N Y
49 C8 H8 C H sing 1.08 N N
50 N7 C5 N C sing 1.37 N Y
51 C5 C6 C C sing 1.39 N Y
52 C5 C4 C C doub 1.39 N Y
53 C4 N3 C N sing 1.34 N Y
54 N3 C2 N C doub 1.35 N Y
55 C2 N1 C N sing 1.36 N Y
56 C2 H2 C H sing 1.08 N N
57 N1 C6 N C doub 1.36 N Y
58 C6 N6 C N sing 1.41 N N
59 N6 HN61 N H sing 1.0 N N
60 N6 HN62 N H sing 1.0 N N



KAA : Used in PDB Entries

Total Number of PDB Entries: 9
Ligand Code PDB Entry ID Type Total Distinct
KAA 3a5y Open in New Window Bound ligand 4 1
KAA 3a5z Open in New Window Bound ligand 4 1
KAA 3e9h Open in New Window Bound ligand 4 1
KAA 4eqe Open in New Window Bound ligand 1 1
KAA 6c86 Open in New Window Bound ligand 2 1
KAA 6chd Open in New Window Bound ligand 2 1
KAA 6ilh Open in New Window Bound ligand 2 1
KAA 7ea9 Open in New Window Bound ligand 4 1
KAA 7f6w Open in New Window Bound ligand 1 1