Chemical Components in the PDB

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2KQ : Summary

Code

2KQ

One-letter code

X

Molecule name

(3S)-3-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-3-oxidanyl-butanoic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (3R,5R,9R,19S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,19-tetrahydroxy-8,8,19-trimethyl-10,14-dioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphahenicosan-21-oic acid 3,5-dioxide (non-preferred name)
OpenEye OEToolkits 1.7.6 (3S)-3-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-3-oxidanyl-butanoic acid

Formula

C25 H42 N7 O19 P3 S

Formal charge

0

Molecular weight

869.623 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)CC(O)(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 3.385 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)NCCS[C](C)(O)CC(O)=O
SMILES OpenEye OEToolkits 1.7.6 CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(C)(CC(=O)O)O)O
Canonical SMILES CACTVS 3.385 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)NCCS[C@](C)(O)CC(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@](CC(=O)O)(O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O

IUPAC InChI

InChI=1S/C25H42N7O19P3S/c1-24(2,19(37)22(38)28-5-4-14(33)27-6-7-55-25(3,39)8-15(34)35)10-48-54(45,46)51-53(43,44)47-9-13-18(50-52(40,41)42)17(36)23(49-13)32-12-31-16-20(26)29-11-30-21(16)32/h11-13,17-19,23,36-37,39H,4-10H2,1-3H3,(H,27,33)(H,28,38)(H,34,35)(H,43,44)(H,45,46)(H2,26,29,30)(H2,40,41,42)/t13-,17-,18-,19+,23-,25+/m1/s1

IUPAC InChI key

FIZPFHAKAOWUQH-RCVSXOLZSA-N
2KQ

wwPDB Information

Atom count

97 (55 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-11-20

Last modified at

2014-03-14

Status

Released

Obsoleted

Not Assigned



2KQ : Atoms of Molecule

Total Number of Atoms: 97
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C01 N N N 0 2.12 2.783 -3.14
2 C02 C C02 N N N 0 1.861 4.258 -2.823
3 C03 C C03 N N N 0 0.718 4.774 -3.7
4 C04 C C04 N N N 0 1.477 4.403 -1.349
5 O05 O O05 N N N 0 0.295 3.644 -1.087
6 P06 P P06 N N N 0 -0.394 3.568 0.366
7 O07 O O07 N N N 0 0.603 3.116 1.362
8 O08 O O08 N N N 0 -0.941 5.025 0.777
9 O09 O O09 N N N 0 -1.621 2.527 0.324
10 P10 P P10 N N N 0 -2.494 1.781 1.453
11 O11 O O11 N N N 0 -2.871 2.75 2.506
12 O12 O O12 N N N 0 -1.625 0.592 2.104
13 O13 O O13 N N N 0 -3.825 1.169 0.785
14 C14 C C14 N N N 0 -4.856 0.536 1.544
15 C15 C C15 R N N 0 -5.97 0.071 0.604
16 O16 O O16 N N N 0 -5.513 -1.029 -0.212
17 C17 C C17 R N N 0 -6.713 -1.69 -0.668
18 N18 N N18 N Y N 0 -6.414 -3.064 -1.08
19 C19 C C19 N Y N 0 -5.358 -3.819 -0.664
20 N20 N N20 N Y N 0 -5.399 -4.99 -1.229
21 C21 C C21 N Y N 0 -6.482 -5.062 -2.04
22 C22 C C22 N Y N 0 -7.026 -6.05 -2.878
23 N23 N N23 N N N 0 -6.413 -7.285 -3.006
24 N24 N N24 N Y N 0 -8.142 -5.773 -3.543
25 C25 C C25 N Y N 0 -8.733 -4.598 -3.427
26 N26 N N26 N Y N 0 -8.26 -3.642 -2.655
27 C27 C C27 N Y N 0 -7.149 -3.828 -1.95
28 C28 C C28 R N N 0 -7.653 -1.689 0.558
29 O29 O O29 N N N 0 -9.007 -1.477 0.152
30 C30 C C30 S N N 0 -7.153 -0.504 1.414
31 O31 O O31 N N N 0 -8.182 0.477 1.562
32 P32 P P32 N N N 0 -8.687 1.009 2.995
33 O33 O O33 N N N 0 -7.531 1.519 3.766
34 O34 O O34 N N N 0 -9.755 2.195 2.781
35 O35 O O35 N N N 0 -9.38 -0.199 3.803
36 C36 C C36 R N N 0 3.126 5.07 -3.104
37 O37 O O37 N N N 0 2.843 6.462 -2.949
38 C38 C C38 N N N 0 4.207 4.667 -2.134
39 O39 O O39 N N N 0 4.572 5.442 -1.275
40 N40 N N40 N N N 0 4.769 3.445 -2.221
41 C41 C C41 N N N 0 5.749 3.016 -1.22
42 C42 C C42 N N N 0 6.227 1.6 -1.548
43 C43 C C43 N N N 0 7.236 1.16 -0.519
44 O44 O O44 N N N 0 7.542 1.905 0.388
45 N45 N N45 N N N 0 7.798 -0.062 -0.606
46 C46 C C46 N N N 0 8.778 -0.491 0.394
47 C47 C C47 N N N 0 9.256 -1.907 0.066
48 S48 S S48 N N N 0 10.47 -2.437 1.305
49 C49 C C49 S N N 0 10.911 -4.109 0.755
50 C50 C C50 N N N 0 11.614 -4.03 -0.602
51 O51 O O51 N N N 0 9.726 -4.898 0.633
52 C52 C C52 N N N 0 11.849 -4.752 1.779
53 C53 C C53 N N N 0 13.087 -3.906 1.927
54 O54 O O54 N N N 0 14.119 -4.349 2.662
55 O55 O O55 N N N 0 13.152 -2.829 1.383
56 H1 H H1 N N N 0 1.193 2.22 -3.031
57 H2 H H2 N N N 0 2.484 2.69 -4.163
58 H3 H H3 N N N 0 2.868 2.39 -2.451
59 H4 H H4 N N N 0 0.579 5.841 -3.525
60 H5 H H5 N N N 0 0.962 4.608 -4.75
61 H6 H H6 N N N 0 -0.2 4.242 -3.452
62 H7 H H7 N N N 0 2.291 4.035 -0.724
63 H11 H H11 N N N 0 -4.444 -0.324 2.072
64 H8 H H8 N N N 0 1.293 5.453 -1.124
65 H9 H H9 N N N 0 -1.6 5.385 0.168
66 H10 H H10 N N N 0 -1.342 -0.082 1.47
67 H12 H H12 N N N 0 -5.262 1.244 2.266
68 H13 H H13 N N N 0 -6.306 0.897 -0.023
69 H14 H H14 N N N 0 -7.163 -1.135 -1.491
70 H15 H H15 N N N 0 -4.598 -3.492 0.031
71 H16 H H16 N N N 0 -5.599 -7.476 -2.514
72 H17 H H17 N N N 0 -6.798 -7.959 -3.587
73 H18 H H18 N N N 0 -9.639 -4.414 -3.986
74 H19 H H19 N N N 0 -7.562 -2.624 1.111
75 H20 H H20 N N N 0 -9.352 -2.162 -0.438
76 H21 H H21 N N N 0 -6.814 -0.853 2.389
77 H22 H H22 N N N 0 -10.102 2.565 3.605
78 H23 H H23 N N N 0 -10.146 -0.582 3.355
79 H24 H H24 N N N 0 3.463 4.879 -4.123
80 H25 H H25 N N N 0 2.538 6.706 -2.064
81 H26 H H26 N N N 0 4.524 2.849 -2.946
82 H27 H H27 N N N 0 6.6 3.698 -1.23
83 H28 H H28 N N N 0 5.288 3.024 -0.233
84 H29 H H29 N N N 0 5.377 0.918 -1.539
85 H30 H H30 N N N 0 6.689 1.592 -2.536
86 H31 H H31 N N N 0 7.553 -0.658 -1.331
87 H32 H H32 N N N 0 9.629 0.191 0.385
88 H33 H H33 N N N 0 8.317 -0.483 1.382
89 H34 H H34 N N N 0 8.406 -2.589 0.075
90 H35 H H35 N N N 0 9.718 -1.915 -0.921
91 H36 H H36 N N N 0 12.543 -3.469 -0.498
92 H37 H H37 N N N 0 11.835 -5.038 -0.955
93 H38 H H38 N N N 0 10.965 -3.529 -1.319
94 H39 H H39 N N N 0 9.229 -4.991 1.457
95 H40 H H40 N N N 0 11.342 -4.825 2.741
96 H41 H H41 N N N 0 12.128 -5.749 1.439
97 H42 H H42 N N N 0 14.892 -3.772 2.728



2KQ : Chemical Bonds

Total Number of Bonds: 99
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N24 C25 N C doub 1.32 N Y
2 N24 C22 N C sing 1.33 N Y
3 C25 N26 C N sing 1.32 N Y
4 N23 C22 N C sing 1.38 N N
5 C22 C21 C C doub 1.41 N Y
6 N26 C27 N C doub 1.33 N Y
7 C21 C27 C C sing 1.41 N Y
8 C21 N20 C N sing 1.35 N Y
9 O11 P10 O P doub 1.48 N N
10 C27 N18 C N sing 1.37 N Y
11 O16 C17 O C sing 1.44 N N
12 O16 C15 O C sing 1.44 N N
13 N20 C19 N C doub 1.3 N Y
14 C41 N40 C N sing 1.47 N N
15 C41 C42 C C sing 1.53 N N
16 N18 C19 N C sing 1.36 N Y
17 N18 C17 N C sing 1.47 N N
18 O44 C43 O C doub 1.21 N N
19 C46 N45 C N sing 1.46 N N
20 C46 C47 C C sing 1.53 N N
21 C17 C28 C C sing 1.54 N N
22 N40 C38 N C sing 1.35 N N
23 C43 N45 C N sing 1.35 N N
24 C43 C42 C C sing 1.51 N N
25 P10 O13 P O sing 1.61 N N
26 P10 O09 P O sing 1.61 N N
27 P10 O12 P O sing 1.61 N N
28 C15 C14 C C sing 1.53 N N
29 C15 C30 C C sing 1.54 N N
30 O33 P32 O P doub 1.48 N N
31 C14 O13 C O sing 1.43 N N
32 S48 C47 S C sing 1.81 N N
33 S48 C49 S C sing 1.81 N N
34 O09 P06 O P sing 1.61 N N
35 C38 O39 C O doub 1.21 N N
36 C38 C36 C C sing 1.51 N N
37 O37 C36 O C sing 1.43 N N
38 C50 C49 C C sing 1.53 N N
39 C36 C02 C C sing 1.53 N N
40 C49 C52 C C sing 1.53 N N
41 C49 O51 C O sing 1.43 N N
42 C28 C30 C C sing 1.54 N N
43 C28 O29 C O sing 1.43 N N
44 C30 O31 C O sing 1.43 N N
45 C52 C53 C C sing 1.51 N N
46 P32 O31 P O sing 1.61 N N
47 P32 O34 P O sing 1.61 N N
48 P32 O35 P O sing 1.61 N N
49 P06 O07 P O doub 1.48 N N
50 P06 O05 P O sing 1.61 N N
51 P06 O08 P O sing 1.61 N N
52 O05 C04 O C sing 1.43 N N
53 C02 C04 C C sing 1.53 N N
54 C02 C01 C C sing 1.53 N N
55 C02 C03 C C sing 1.53 N N
56 C53 O55 C O doub 1.21 N N
57 C53 O54 C O sing 1.34 N N
58 C01 H1 C H sing 1.09 N N
59 C01 H2 C H sing 1.09 N N
60 C01 H3 C H sing 1.09 N N
61 C03 H4 C H sing 1.09 N N
62 C03 H5 C H sing 1.09 N N
63 C03 H6 C H sing 1.09 N N
64 C04 H7 C H sing 1.09 N N
65 C04 H8 C H sing 1.09 N N
66 O08 H9 O H sing 0.97 N N
67 O12 H10 O H sing 0.97 N N
68 C14 H11 C H sing 1.09 N N
69 C14 H12 C H sing 1.09 N N
70 C15 H13 C H sing 1.09 N N
71 C17 H14 C H sing 1.09 N N
72 C19 H15 C H sing 1.08 N N
73 N23 H16 N H sing 0.97 N N
74 N23 H17 N H sing 0.97 N N
75 C25 H18 C H sing 1.08 N N
76 C28 H19 C H sing 1.09 N N
77 O29 H20 O H sing 0.97 N N
78 C30 H21 C H sing 1.09 N N
79 O34 H22 O H sing 0.97 N N
80 O35 H23 O H sing 0.97 N N
81 C36 H24 C H sing 1.09 N N
82 O37 H25 O H sing 0.97 N N
83 N40 H26 N H sing 0.97 N N
84 C41 H27 C H sing 1.09 N N
85 C41 H28 C H sing 1.09 N N
86 C42 H29 C H sing 1.09 N N
87 C42 H30 C H sing 1.09 N N
88 N45 H31 N H sing 0.97 N N
89 C46 H32 C H sing 1.09 N N
90 C46 H33 C H sing 1.09 N N
91 C47 H34 C H sing 1.09 N N
92 C47 H35 C H sing 1.09 N N
93 C50 H36 C H sing 1.09 N N
94 C50 H37 C H sing 1.09 N N
95 C50 H38 C H sing 1.09 N N
96 O51 H39 O H sing 0.97 N N
97 C52 H40 C H sing 1.09 N N
98 C52 H41 C H sing 1.09 N N
99 O54 H42 O H sing 0.97 N N



2KQ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
2KQ 4nnc Open in New Window Bound ligand 1 1