Chemical Components in the PDB

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FYN : Summary

Code

FYN

One-letter code

X

Molecule name

S-{(9R,13S,15R)-17-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-9,13,15-TRIHYDROXY-10,10-DIMETHYL-13,15-DIOXIDO-4,8-DIOXO-12,14,16-TRIOXA-3,7-DIAZA-13,15-DIPHOSPHAHEPTADEC-1-YL} THIOFORMATE

Systematic names

ProgramVersionName
ACDLabs 10.04 S-{(9R,13S,15R)-17-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-9,13,15-trihydroxy-10,10-dimethyl-13,15-dioxido-4,8-dioxo-12,14,16-trioxa-3,7-diaza-13,15-diphosphaheptadec-1-yl} thioformate (non-preferred name)
OpenEye OEToolkits 1.5.0 S-[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]ethyl] methanethioate

Formula

C22 H36 N7 O17 P3 S

Formal charge

0

Molecular weight

795.544 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=CSCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
SMILES CACTVS 3.341 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)NCCSC=O
SMILES OpenEye OEToolkits 1.5.0 CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC=O)O
Canonical SMILES CACTVS 3.341 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)NCCSC=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(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)[C@H](C(=O)NCCC(=O)NCCSC=O)O

IUPAC InChI

InChI=1S/C22H36N7O17P3S/c1-22(2,17(33)20(34)25-4-3-13(31)24-5-6-50-11-30)8-43-49(40,41)46-48(38,39)42-7-12-16(45-47(35,36)37)15(32)21(44-12)29-10-28-14-18(23)26-9-27-19(14)29/h9-12,15-17,21,32-33H,3-8H2,1-2H3,(H,24,31)(H,25,34)(H,38,39)(H,40,41)(H2,23,26,27)(H2,35,36,37)/t12-,15-,16-,17+,21-/m1/s1

IUPAC InChI key

SXMOKYXNAPLNCW-GORZOVPNSA-N
FYN

wwPDB Information

Atom count

86 (50 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2007-02-26

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



FYN : Atoms of Molecule

Total Number of Atoms: 86
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C8 C C8 N Y N 0 10.177 1.752 6.199
2 N9 N N9 N Y N 0 10.737 0.512 6.036
3 C4 C C4 N Y N 0 11.861 0.475 6.812
4 C5 C C5 N Y N 0 11.926 1.72 7.418
5 N7 N N7 N Y N 0 10.871 2.506 7.027
6 N3 N N3 N Y N 0 12.72 -0.545 6.959
7 C2 C C2 N Y N 0 13.712 -0.207 7.812
8 N1 N N1 N Y N 0 13.905 0.96 8.472
9 C6 C C6 N Y N 0 12.997 1.947 8.276
10 N6 N N6 N N N 0 13.142 3.181 8.932
11 C1' C C1' R N N 0 10.22 -0.563 5.186
12 C2' C C2' R N N 0 9.179 -1.445 5.879
13 O2' O O2' N N N 0 9.419 -2.81 5.54
14 C3' C C3' S N N 0 7.872 -0.953 5.285
15 O3' O O3' N N N 0 6.852 -1.929 5.287
16 C4' C C4' R N N 0 8.285 -0.56 3.877
17 O4' O O4' N N N 0 9.598 0.007 4.015
18 C5' C C5' N N N 0 7.353 0.451 3.234
19 O5' O O5' N N N 0 7.83 0.757 1.935
20 P1 P P1 S N N 0 7.031 1.815 1.007
21 O11 O O11 N N N 0 5.51 1.264 0.973
22 O12 O O12 N N N 0 7.632 2.057 -0.346
23 O6 O O6 N N N 0 6.94 3.126 1.949
24 P2 P P2 R N N 0 8.093 4.108 2.513
25 O21 O O21 N N N 0 8.666 4.82 1.179
26 O22 O O22 N N N 0 9.129 3.445 3.373
27 O7 O O7 N N N 0 7.2 5.25 3.225
28 CPB C CPB N N N 0 6.203 5.908 2.449
29 CPA C CPA N N N 0 5.451 6.967 3.293
30 CP7 C CP7 R N N 0 4.745 6.312 4.517
31 CP9 C CP9 N N N 0 6.471 8.008 3.811
32 CP8 C CP8 N N N 0 4.437 7.715 2.405
33 OP3 O OP3 N N N 0 4.06 7.312 5.267
34 CP6 C CP6 N N N 0 3.704 5.256 4.152
35 OP2 O OP2 N N N 0 2.511 5.39 4.417
36 NP2 N NP2 N N N 0 4.251 4.174 3.481
37 CP5 C CP5 N N N 0 3.461 3.06 3.009
38 CP4 C CP4 N N N 0 3.382 1.99 4.089
39 CP3 C CP3 N N N 0 2.577 0.78 3.651
40 OP1 O OP1 N N N 0 2.051 0.687 2.545
41 NP1 N NP1 N N N 0 2.517 -0.182 4.649
42 CP2 C CP2 N N N 0 1.81 -1.431 4.492
43 CP1 C CP1 N N N 0 0.354 -1.351 4.931
44 S S S N N N 0 0.189 -0.935 6.694
45 P3 P P3 N N N 0 6.383 -2.538 6.706
46 O31 O O31 N N N 0 7.459 -3.232 7.489
47 O32 O O32 N N N 0 5.103 -3.452 6.331
48 O33 O O33 N N N 0 5.723 -1.257 7.439
49 CM1 C CM1 N N N 0 -1.558 -1.018 6.833
50 OM2 O OM2 N N N 0 -2.125 -0.799 7.896
51 H8 H H8 N N N 0 9.269 2.047 5.691
52 H1' H H1' N N N 0 11.103 -1.126 4.867
53 H2 H H2 N N N 0 14.458 -0.975 7.991
54 H6N1 H 1H6N N N N 0 13.326 4.007 8.394
55 H6N2 H 2H6N N N N 0 13.154 3.208 9.934
56 H2' H H2' N N N 0 9.196 -1.38 6.971
57 HA H HA N N N 0 8.68 -3.331 5.898
58 H3' H H3' N N N 0 7.526 -0.073 5.839
59 H4' H H4' N N N 0 8.356 -1.438 3.224
60 H5'1 H 1H5' N N N 0 7.32 1.372 3.823
61 H5'2 H 2H5' N N N 0 6.342 0.042 3.15
62 H11 H H11 N N N 0 4.862 1.699 0.378
63 H21 H H21 N N N 0 9.28 4.321 0.6
64 HPB1 H 1HPB N N N 0 6.706 6.373 1.595
65 HPB2 H 2HPB N N N 0 5.516 5.145 2.071
66 HP7 H HP7 N N N 0 5.494 5.866 5.184
67 HP91 H 1HP9 N N N 0 5.983 8.746 4.458
68 HP92 H 2HP9 N N N 0 6.943 8.557 2.988
69 HP93 H 3HP9 N N N 0 7.271 7.534 4.389
70 HP81 H 1HP8 N N N 0 4.939 8.297 1.624
71 HP82 H 2HP8 N N N 0 3.835 8.414 2.996
72 HP83 H 3HP8 N N N 0 3.755 7.022 1.899
73 HP3 H HP3 N N N 0 3.226 7.482 4.802
74 HP2 H HP2 N N N 0 5.246 4.162 3.28
75 HP51 H 1HP5 N N N 0 2.459 3.414 2.743
76 HP52 H 2HP5 N N N 0 3.915 2.654 2.098
77 HP41 H 1HP4 N N N 0 2.92 2.404 4.994
78 HP42 H 2HP4 N N N 0 4.391 1.654 4.36
79 HP1 H HP1 N N N 0 2.991 0.001 5.529
80 HP21 H 1HP2 N N N 0 1.854 -1.683 3.427
81 HP22 H 2HP2 N N N 0 2.36 -2.203 5.04
82 HP11 H 1HP1 N N N 0 -0.19 -0.602 4.346
83 HP12 H 2HP1 N N N 0 -0.13 -2.32 4.773
84 HM1 H HM1 N N N 0 -2.124 -1.278 5.925
85 H32 H H32 N N N 0 4.677 -3.984 7.036
86 H33 H H33 N N N 0 5.436 -1.34 8.373



FYN : Chemical Bonds

Total Number of Bonds: 88
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C8 N9 C N sing 1.37 N Y
2 N9 C4 N C sing 1.37 N Y
3 C4 C5 C C sing 1.39 N Y
4 C8 N7 C N doub 1.32 N Y
5 C5 N7 C N sing 1.37 N Y
6 C4 N3 C N doub 1.34 N Y
7 N3 C2 N C sing 1.35 N Y
8 C2 N1 C N doub 1.35 N Y
9 C5 C6 C C doub 1.39 N Y
10 N1 C6 N C sing 1.36 N Y
11 C6 N6 C N sing 1.41 N N
12 N9 C1' N C sing 1.46 N N
13 C1' C2' C C sing 1.53 N N
14 C2' O2' C O sing 1.43 N N
15 C2' C3' C C sing 1.52 N N
16 C3' O3' C O sing 1.41 N N
17 C3' C4' C C sing 1.52 N N
18 C1' O4' C O sing 1.44 N N
19 C4' O4' C O sing 1.44 N N
20 C4' C5' C C sing 1.52 N N
21 C5' O5' C O sing 1.42 N N
22 O5' P1 O P sing 1.62 N N
23 P1 O11 P O sing 1.62 N N
24 P1 O12 P O doub 1.5 N N
25 P1 O6 P O sing 1.62 N N
26 O6 P2 O P sing 1.62 N N
27 P2 O21 P O sing 1.62 N N
28 P2 O22 P O doub 1.5 N N
29 P2 O7 P O sing 1.62 N N
30 O7 CPB O C sing 1.42 N N
31 CPB CPA C C sing 1.55 N N
32 CPA CP7 C C sing 1.56 N N
33 CPA CP9 C C sing 1.55 N N
34 CPA CP8 C C sing 1.54 N N
35 CP7 OP3 C O sing 1.43 N N
36 CP7 CP6 C C sing 1.53 N N
37 CP6 OP2 C O doub 1.23 N N
38 CP6 NP2 C N sing 1.39 N N
39 NP2 CP5 N C sing 1.44 N N
40 CP5 CP4 C C sing 1.52 N N
41 CP4 CP3 C C sing 1.52 N N
42 CP3 OP1 C O doub 1.23 N N
43 CP3 NP1 C N sing 1.39 N N
44 NP1 CP2 N C sing 1.44 N N
45 CP2 CP1 C C sing 1.52 N N
46 CP1 S C S sing 1.82 N N
47 O3' P3 O P sing 1.61 N N
48 P3 O31 P O doub 1.5 N N
49 P3 O32 P O sing 1.62 N N
50 P3 O33 P O sing 1.62 N N
51 S CM1 S C sing 1.75 N N
52 CM1 OM2 C O doub 1.22 N N
53 C8 H8 C H sing 1.08 N N
54 C1' H1' C H sing 1.09 N N
55 C2 H2 C H sing 1.09 N N
56 N6 H6N1 N H sing 1.0 N N
57 N6 H6N2 N H sing 1.0 N N
58 C2' H2' C H sing 1.09 N N
59 O2' HA O H sing 0.97 N N
60 C3' H3' C H sing 1.1 N N
61 C4' H4' C H sing 1.1 N N
62 C5' H5'1 C H sing 1.09 N N
63 C5' H5'2 C H sing 1.09 N N
64 O11 H11 O H sing 0.98 N N
65 O21 H21 O H sing 0.98 N N
66 CPB HPB1 C H sing 1.09 N N
67 CPB HPB2 C H sing 1.09 N N
68 CP7 HP7 C H sing 1.1 N N
69 CP9 HP91 C H sing 1.1 N N
70 CP9 HP92 C H sing 1.1 N N
71 CP9 HP93 C H sing 1.09 N N
72 CP8 HP81 C H sing 1.1 N N
73 CP8 HP82 C H sing 1.1 N N
74 CP8 HP83 C H sing 1.1 N N
75 OP3 HP3 O H sing 0.97 N N
76 NP2 HP2 N H sing 1.02 N N
77 CP5 HP51 C H sing 1.1 N N
78 CP5 HP52 C H sing 1.1 N N
79 CP4 HP41 C H sing 1.1 N N
80 CP4 HP42 C H sing 1.1 N N
81 NP1 HP1 N H sing 1.02 N N
82 CP2 HP21 C H sing 1.1 N N
83 CP2 HP22 C H sing 1.09 N N
84 CP1 HP11 C H sing 1.1 N N
85 CP1 HP12 C H sing 1.09 N N
86 CM1 HM1 C H sing 1.1 N N
87 O32 H32 O H sing 0.98 N N
88 O33 H33 O H sing 0.98 N N



FYN : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
FYN 2ji8 Open in New Window Bound ligand 2 1
FYN 7pt4 Open in New Window Bound ligand 1 1