Chemical Components in the PDB

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TAP : Summary

Code

TAP

One-letter code

X

Molecule name

7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Synonyms

TATP

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.5.0 [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-4-phosphonooxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3S,4R,5R)-5-(3-carbamothioylpyridin-1-ium-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl phosphate

Formula

C21 H28 N7 O16 P3 S

Formal charge

0

Molecular weight

759.471 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.341 NC(=S)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 1.5.0 c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=S)N
Canonical SMILES CACTVS 3.341 NC(=S)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=S)N

IUPAC InChI

InChI=1S/C21H28N7O16P3S/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(43-45(32,33)34)14(30)11(42-21)6-40-47(37,38)44-46(35,36)39-5-10-13(29)15(31)20(41-10)27-3-1-2-9(4-27)18(23)48/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,48)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1

IUPAC InChI key

OJNFDOAQUXJWED-NNYOXOHSSA-N
TAP

wwPDB Information

Atom count

76 (48 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



TAP : Atoms of Molecule

Total Number of Atoms: 76
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 PA P AP R N N 0 -0.318 -1.061 0.687
2 O1A O AO1 N N N 0 0.196 -0.446 1.931
3 O2A O AO2 N N N 0 -1.026 -2.465 1.036
4 O5B O AO5* N N N 0 -1.391 -0.074 0.004
5 C5B C AC5* N N N 0 -2.384 0.205 0.993
6 C4B C AC4* R N N 0 -3.439 1.144 0.405
7 O4B O AO4* N N N 0 -4.171 0.469 -0.632
8 C3B C AC3* R N N 0 -4.45 1.545 1.497
9 O3B O AO3* N N N 0 -4.454 2.962 1.688
10 C2B C AC2* R N N 0 -5.816 1.069 0.938
11 O2B O AO2* N N N 0 -6.837 2.036 1.196
12 C1B C AC1* R N N 0 -5.527 0.963 -0.581
13 N9A N AN9 N Y N 0 -6.445 0.017 -1.22
14 C8A C AC8 N Y N 0 -6.237 -1.32 -1.389
15 N7A N AN7 N Y N 0 -7.257 -1.856 -1.993
16 C5A C AC5 N Y N 0 -8.182 -0.9 -2.25
17 C6A C AC6 N Y N 0 -9.446 -0.887 -2.863
18 N6A N AN6 N N N 0 -10.0 -2.051 -3.367
19 N1A N AN1 N Y N 0 -10.098 0.268 -2.947
20 C2A C AC2 N Y N 0 -9.578 1.383 -2.468
21 N3A N AN3 N Y N 0 -8.397 1.419 -1.887
22 C4A C AC4 N Y N 0 -7.674 0.312 -1.752
23 O3 O O3 N N N 0 0.903 -1.315 -0.331
24 PN P NP N N N 0 2.101 -1.959 0.53
25 O1N O NO1 N N N 0 1.835 -3.467 0.734
26 O2N O NO2 N N N -1 2.181 -1.26 1.905
27 O5D O NO5* N N N 0 3.493 -1.761 -0.255
28 C5D C NC5* N N N 0 4.525 -2.244 0.607
29 C4D C NC4* R N N 0 5.881 -2.083 -0.082
30 O4D O NO4* N N N 0 6.199 -0.684 -0.247
31 C3D C NC3* S N N 0 7.011 -2.642 0.811
32 C1D C NC1* R N N 0 7.632 -0.638 -0.427
33 O3D O NO3* N N N 0 7.363 -3.966 0.404
34 C2D C NC2* R N N 0 8.191 -1.67 0.578
35 O2D O NO2* N N N 0 9.309 -2.364 0.021
36 N1N N NN1 N Y N 1 8.141 0.701 -0.12
37 C2N C NC2 N Y N 0 9.125 1.192 -0.844
38 C3N C NC3 N Y N 0 9.638 2.462 -0.575
39 S7N S NS7 N N N 0 11.971 1.973 -1.973
40 C7N C NC7 N N N 0 10.744 3.012 -1.384
41 N7N N NN7 N N N 0 10.789 4.33 -1.658
42 C4N C NC4 N Y N 0 9.082 3.209 0.471
43 C5N C NC5 N Y N 0 8.047 2.649 1.198
44 C6N C NC6 N Y N 0 7.598 1.381 0.872
45 P2B P AP2* N N N 0 -8.043 1.257 1.924
46 O1X O AOP1 N N N 0 -7.526 0.56 3.124
47 O2X O AOP2 N N N 0 -9.176 2.313 2.363
48 O3X O AOP3 N N N 0 -8.677 0.18 0.909
49 HOA2 H 2HOA N N N 0 -1.347 -2.831 0.2
50 H51A H AH51 N N N 0 -2.858 -0.725 1.304
51 H52A H AH52 N N N 0 -1.914 0.68 1.854
52 H4B H AH4* N N N 0 -2.959 2.034 -0.001
53 H3B H AH3* N N N 0 -4.222 1.036 2.433
54 HO3A H AHO3 N N N 0 -3.583 3.199 2.035
55 H2B H AH2* N N N 0 -6.09 0.098 1.351
56 H1B H AH1* N N N 0 -5.596 1.942 -1.055
57 H8A H AH8 N N N 0 -5.356 -1.855 -1.068
58 H61A H AH61 N N N 0 -9.515 -2.888 -3.3
59 H62A H AH62 N N N 0 -10.874 -2.029 -3.788
60 H2A H AH2 N N N 0 -10.141 2.3 -2.558
61 H51N H NH51 N N N 0 4.352 -3.297 0.827
62 H52N H NH52 N N N 0 4.52 -1.673 1.535
63 H4D H NH4* N N N 0 5.877 -2.588 -1.049
64 H3D H NH3* N N N 0 6.709 -2.634 1.858
65 HO3N H NHO3 N N N 0 8.07 -4.261 0.994
66 H2D H NH2* N N N 0 8.473 -1.18 1.51
67 HO2N H NHO2 N N N 0 9.573 -3.033 0.668
68 H1D H NH1* N N N 0 7.896 -0.919 -1.446
69 H2N H NH2 N N N 0 9.543 0.605 -1.648
70 H71N H NH71 N N N 0 11.515 4.691 -2.189
71 H72N H NH72 N N N 0 10.091 4.918 -1.327
72 H4N H NH4 N N N 0 9.452 4.196 0.705
73 H5N H NH5 N N N 0 7.594 3.195 2.012
74 H6N H NH6 N N N 0 6.791 0.941 1.438
75 HOP2 H 2HOP N N N 0 -9.878 1.807 2.795
76 HOP3 H 3HOP N N N 0 -9.0 0.675 0.144



TAP : Chemical Bonds

Total Number of Bonds: 80
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 PA O1A P O doub 1.48 N N
2 PA O2A P O sing 1.61 N N
3 PA O5B P O sing 1.61 N N
4 PA O3 P O sing 1.61 N N
5 O2A HOA2 O H sing 0.97 N N
6 O5B C5B O C sing 1.43 N N
7 C5B C4B C C sing 1.53 N N
8 C5B H51A C H sing 1.09 N N
9 C5B H52A C H sing 1.09 N N
10 C4B O4B C O sing 1.44 N N
11 C4B C3B C C sing 1.54 N N
12 C4B H4B C H sing 1.09 N N
13 O4B C1B O C sing 1.44 N N
14 C3B O3B C O sing 1.43 N N
15 C3B C2B C C sing 1.55 N N
16 C3B H3B C H sing 1.09 N N
17 O3B HO3A O H sing 0.97 N N
18 C2B O2B C O sing 1.43 N N
19 C2B C1B C C sing 1.55 N N
20 C2B H2B C H sing 1.09 N N
21 O2B P2B O P sing 1.61 N N
22 C1B N9A C N sing 1.46 N N
23 C1B H1B C H sing 1.09 N N
24 N9A C8A N C sing 1.36 N Y
25 N9A C4A N C sing 1.37 N Y
26 C8A N7A C N doub 1.3 N Y
27 C8A H8A C H sing 1.08 N N
28 N7A C5A N C sing 1.35 N Y
29 C5A C6A C C sing 1.4 N Y
30 C5A C4A C C doub 1.41 N Y
31 C6A N6A C N sing 1.38 N N
32 C6A N1A C N doub 1.33 N Y
33 N6A H61A N H sing 0.97 N N
34 N6A H62A N H sing 0.97 N N
35 N1A C2A N C sing 1.32 N Y
36 C2A N3A C N doub 1.32 N Y
37 C2A H2A C H sing 1.08 N N
38 N3A C4A N C sing 1.33 N Y
39 O3 PN O P sing 1.61 N N
40 PN O1N P O doub 1.54 N N
41 PN O2N P O sing 1.54 N N
42 PN O5D P O sing 1.61 N N
43 O5D C5D O C sing 1.43 N N
44 C5D C4D C C sing 1.53 N N
45 C5D H51N C H sing 1.09 N N
46 C5D H52N C H sing 1.09 N N
47 C4D O4D C O sing 1.44 N N
48 C4D C3D C C sing 1.54 N N
49 C4D H4D C H sing 1.09 N N
50 O4D C1D O C sing 1.44 N N
51 C3D O3D C O sing 1.43 N N
52 C3D C2D C C sing 1.55 N N
53 C3D H3D C H sing 1.09 N N
54 O3D HO3N O H sing 0.97 N N
55 C2D O2D C O sing 1.43 N N
56 C2D C1D C C sing 1.55 N N
57 C2D H2D C H sing 1.09 N N
58 O2D HO2N O H sing 0.97 N N
59 C1D N1N C N sing 1.47 N N
60 C1D H1D C H sing 1.09 N N
61 N1N C2N N C sing 1.32 N Y
62 N1N C6N N C doub 1.32 N Y
63 C2N C3N C C doub 1.4 N Y
64 C2N H2N C H sing 1.08 N N
65 C3N C7N C C sing 1.48 N N
66 C3N C4N C C sing 1.4 N Y
67 C7N S7N C S doub 1.71 N N
68 C7N N7N C N sing 1.35 N N
69 N7N H71N N H sing 0.97 N N
70 N7N H72N N H sing 0.97 N N
71 C4N C5N C C doub 1.38 N Y
72 C4N H4N C H sing 1.08 N N
73 C5N C6N C C sing 1.38 N Y
74 C5N H5N C H sing 1.08 N N
75 C6N H6N C H sing 1.08 N N
76 P2B O1X P O doub 1.48 N N
77 P2B O2X P O sing 1.61 N N
78 P2B O3X P O sing 1.61 N N
79 O2X HOP2 O H sing 0.97 N N
80 O3X HOP3 O H sing 0.97 N N



TAP : Used in PDB Entries

Total Number of PDB Entries: 6
Ligand Code PDB Entry ID Type Total Distinct
TAP 1dr2 Open in New Window Bound ligand 1 1
TAP 1dr3 Open in New Window Bound ligand 1 1
TAP 1pt9 Open in New Window Bound ligand 2 1
TAP 4aja Open in New Window Bound ligand 1 1
TAP 4ajb Open in New Window Bound ligand 1 1
TAP 4go2 Open in New Window Bound ligand 4 1