Chemical Components in the PDB

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R6G : Summary

Code

R6G

One-letter code

X

Molecule name

RHODAMINE 6G

Systematic names

ProgramVersionName
ACDLabs 10.04 2-[(3S)-3,6-bis(ethylamino)-2,7-dimethyl-3H-xanthen-9-yl]-5-[(6-hydroxyhexyl)carbamoyl]benzoic acid
OpenEye OEToolkits 1.5.0 2-[(3S)-3,6-bis(ethylamino)-2,7-dimethyl-3H-xanthen-9-yl]-5-(6-hydroxyhexylcarbamoyl)benzoic acid

Formula

C33 H41 N3 O5

Formal charge

0

Molecular weight

559.696 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(NCCCCCCO)c4ccc(C=1c3c(OC=2C=1C=C(C)C(NCC)C=2)cc(c(c3)C)NCC)c(C(=O)O)c4
SMILES CACTVS 3.385 CCN[CH]1C=C2Oc3cc(NCC)c(C)cc3C(=C2C=C1C)c4ccc(cc4C(O)=O)C(=O)NCCCCCCO
SMILES OpenEye OEToolkits 1.7.5 CCNc1cc2c(cc1C)C(=C3C=C(C(C=C3O2)NCC)C)c4ccc(cc4C(=O)O)C(=O)NCCCCCCO
Canonical SMILES CACTVS 3.385 CCN[C@H]1C=C2Oc3cc(NCC)c(C)cc3C(=C2C=C1C)c4ccc(cc4C(O)=O)C(=O)NCCCCCCO
Canonical SMILES OpenEye OEToolkits 1.7.5 CCNc1cc2c(cc1C)C(=C3C=C([C@H](C=C3O2)NCC)C)c4ccc(cc4C(=O)O)C(=O)NCCCCCCO

IUPAC InChI

InChI=1S/C33H41N3O5/c1-5-34-27-18-29-25(15-20(27)3)31(26-16-21(4)28(35-6-2)19-30(26)41-29)23-12-11-22(17-24(23)33(39)40)32(38)36-13-9-7-8-10-14-37/h11-12,15-19,27,34-35,37H,5-10,13-14H2,1-4H3,(H,36,38)(H,39,40)/t27-/m0/s1

IUPAC InChI key

INWCCTLLQCEQJQ-MHZLTWQESA-N
R6G

wwPDB Information

Atom count

82 (41 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2007-06-19

Last modified at

2012-01-05

Status

Released

Obsoleted

Not Assigned



R6G : Atoms of Molecule

Total Number of Atoms: 82
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C N N N 0 -11.755 -0.356 -1.698
2 O O O N N N 0 -13.108 -0.424 -1.243
3 N N N N N N 0 5.222 -4.325 -0.395
4 N1 N N1 N N N 0 4.185 3.989 0.3
5 C1 C C1 N Y N 0 4.748 -2.076 -1.115
6 C2 C C2 N Y N 0 3.903 -0.98 -1.152
7 C3 C C3 N Y N 0 2.669 -1.036 -0.486
8 C4 C C4 N Y N 0 2.292 -2.192 0.195
9 C5 C C5 N Y N 0 3.139 -3.279 0.221
10 C6 C C6 N Y N 0 4.367 -3.223 -0.43
11 C7 C C7 N N N 0 1.778 0.149 -0.498
12 C8 C C8 N N N 0 2.317 1.325 -0.991
13 C9 C C9 N N N 0 3.704 1.314 -1.501
14 O1 O O1 N N N 0 4.269 0.131 -1.845
15 C10 C C10 N N N 0 4.367 2.47 -1.57
16 C11 C C11 R N N 0 3.752 3.75 -1.083
17 C12 C C12 N N N 0 2.254 3.725 -1.124
18 C13 C C13 N N N 0 1.565 2.584 -1.062
19 C14 C C14 N Y N 0 0.391 0.077 -0.012
20 C15 C C15 N Y N 0 -0.671 0.063 -0.921
21 C16 C C16 N Y N 0 -1.959 -0.003 -0.474
22 C17 C C17 N Y N 0 -2.232 -0.057 0.898
23 C18 C C18 N Y N 0 -1.189 -0.044 1.822
24 C19 C C19 N Y N 0 0.128 0.017 1.375
25 C20 C C20 N N N 0 1.503 5.027 -1.237
26 C21 C C21 N N N 0 2.734 -4.531 0.956
27 C22 C C22 N N N 0 1.241 0.026 2.342
28 O2 O O2 N N N 0 0.985 -0.032 3.664
29 O3 O O3 N N N 0 2.388 0.084 1.947
30 C23 C C23 N N N 0 -3.63 -0.128 1.368
31 O4 O O4 N N N 0 -3.87 -0.175 2.559
32 N2 N N2 N N N 0 -4.641 -0.14 0.476
33 C24 C C24 N N N 0 -6.028 -0.21 0.942
34 C25 C C25 N N N 0 -6.971 -0.21 -0.262
35 C26 C C26 N N N 0 -8.42 -0.283 0.225
36 C27 C C27 N N N 0 -9.363 -0.283 -0.98
37 C28 C C28 N N N 0 -10.812 -0.356 -0.493
38 C29 C C29 N N N 0 5.488 4.667 0.335
39 C30 C C30 N N N 0 5.905 4.897 1.789
40 C31 C C31 N N N 0 6.516 -4.27 -1.079
41 C32 C C32 N N N 0 7.251 -5.598 -0.887
42 HC1 H 1HC N N N 0 -11.54 -1.219 -2.328
43 HC2 H 2HC N N N 0 -11.611 0.559 -2.272
44 H281 H 1H28 N N N 0 -11.028 0.507 0.137
45 H282 H 2H28 N N N 0 -10.956 -1.271 0.081
46 H H H N N N 0 4.959 -5.127 0.082
47 H311 H 1H31 N N N 0 6.358 -4.094 -2.143
48 H312 H 2H31 N N N 0 7.114 -3.46 -0.661
49 H1 H H1 N N N 0 3.491 4.512 0.811
50 H291 H 1H29 N N N 0 6.234 4.047 -0.163
51 H292 H 2H29 N N N 0 5.411 5.626 -0.178
52 HA H HA N N N 0 5.701 -2.041 -1.622
53 H4 H H4 N N N 0 1.338 -2.236 0.701
54 H211 H 1H21 N N N 0 2.199 -5.194 0.277
55 H212 H 2H21 N N N 0 3.624 -5.036 1.331
56 H213 H 3H21 N N N 0 2.086 -4.268 1.793
57 H13 H H13 N N N 0 0.485 2.586 -1.065
58 H10 H H10 N N N 0 5.365 2.484 -1.984
59 H201 H 1H20 N N N 0 1.351 5.269 -2.289
60 H202 H 2H20 N N N 0 0.536 4.933 -0.742
61 H203 H 3H20 N N N 0 2.079 5.821 -0.761
62 H15 H H15 N N N 0 -0.471 0.105 -1.982
63 H16 H H16 N N N 0 -2.773 -0.014 -1.184
64 H18 H H18 N N N 0 -1.401 -0.085 2.88
65 H2 H H2 N N N 0 1.747 -0.023 4.259
66 HB H HB N N N 0 -4.45 -0.102 -0.474
67 H241 H 1H24 N N N 0 -6.172 -1.125 1.517
68 H242 H 2H24 N N N 0 -6.243 0.653 1.573
69 H251 H 1H25 N N N 0 -6.827 0.705 -0.837
70 H252 H 2H25 N N N 0 -6.756 -1.073 -0.893
71 H261 H 1H26 N N N 0 -8.564 -1.198 0.799
72 H262 H 2H26 N N N 0 -8.635 0.58 0.855
73 H271 H 1H27 N N N 0 -9.219 0.632 -1.555
74 H272 H 2H27 N N N 0 -9.148 -1.146 -1.61
75 H323 H 3H32 N N N 0 8.214 -5.557 -1.396
76 H301 H 1H30 N N N 0 5.159 5.517 2.287
77 H302 H 2H30 N N N 0 5.981 3.938 2.301
78 H303 H 3H30 N N N 0 6.871 5.401 1.814
79 H321 H 1H32 N N N 0 7.41 -5.775 0.177
80 H322 H 2H32 N N N 0 6.654 -6.408 -1.304
81 HO1 H 1HO N N N 0 -13.763 -0.428 -1.955
82 H11 H H11 N N N 0 4.106 4.57 -1.708



R6G : Chemical Bonds

Total Number of Bonds: 85
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C O C O sing 1.43 N N
2 C C28 C C sing 1.53 N N
3 C HC1 C H sing 1.09 N N
4 C HC2 C H sing 1.09 N N
5 O HO1 O H sing 0.97 N N
6 N C6 N C sing 1.4 N N
7 N C31 N C sing 1.46 N N
8 N H N H sing 0.97 N N
9 N1 C11 N C sing 1.47 N N
10 N1 C29 N C sing 1.47 N N
11 N1 H1 N H sing 1.01 N N
12 C1 C2 C C doub 1.38 N Y
13 C1 C6 C C sing 1.39 N Y
14 C1 HA C H sing 1.08 N N
15 C2 C3 C C sing 1.4 N Y
16 C2 O1 C O sing 1.36 N N
17 C3 C4 C C doub 1.39 N Y
18 C3 C7 C C sing 1.48 N N
19 C4 C5 C C sing 1.38 N Y
20 C4 H4 C H sing 1.08 N N
21 C5 C6 C C doub 1.39 N Y
22 C5 C21 C C sing 1.51 N N
23 C7 C8 C C doub 1.38 N N
24 C7 C14 C C sing 1.47 N N
25 C8 C9 C C sing 1.48 N N
26 C8 C13 C C sing 1.47 N N
27 C9 O1 C O sing 1.36 N N
28 C9 C10 C C doub 1.33 N N
29 C10 C11 C C sing 1.5 N N
30 C10 H10 C H sing 1.08 N N
31 C11 H11 C H sing 1.09 N N
32 C11 C12 C C sing 1.5 N N
33 C12 C13 C C doub 1.33 N N
34 C12 C20 C C sing 1.51 N N
35 C13 H13 C H sing 1.08 N N
36 C14 C15 C C sing 1.4 N Y
37 C14 C19 C C doub 1.41 N Y
38 C15 C16 C C doub 1.36 N Y
39 C15 H15 C H sing 1.08 N N
40 C16 C17 C C sing 1.4 N Y
41 C16 H16 C H sing 1.08 N N
42 C17 C18 C C doub 1.39 N Y
43 C17 C23 C C sing 1.48 N N
44 C18 C19 C C sing 1.39 N Y
45 C18 H18 C H sing 1.08 N N
46 C19 C22 C C sing 1.47 N N
47 C20 H201 C H sing 1.09 N N
48 C20 H202 C H sing 1.09 N N
49 C20 H203 C H sing 1.09 N N
50 C21 H211 C H sing 1.09 N N
51 C21 H212 C H sing 1.09 N N
52 C21 H213 C H sing 1.09 N N
53 C22 O2 C O sing 1.35 N N
54 C22 O3 C O doub 1.21 N N
55 O2 H2 O H sing 0.97 N N
56 C23 O4 C O doub 1.22 N N
57 C23 N2 C N sing 1.35 N N
58 N2 C24 N C sing 1.46 N N
59 N2 HB N H sing 0.97 N N
60 C24 C25 C C sing 1.53 N N
61 C24 H241 C H sing 1.09 N N
62 C24 H242 C H sing 1.09 N N
63 C25 C26 C C sing 1.53 N N
64 C25 H251 C H sing 1.09 N N
65 C25 H252 C H sing 1.09 N N
66 C26 C27 C C sing 1.53 N N
67 C26 H261 C H sing 1.09 N N
68 C26 H262 C H sing 1.09 N N
69 C27 C28 C C sing 1.53 N N
70 C27 H271 C H sing 1.09 N N
71 C27 H272 C H sing 1.09 N N
72 C28 H281 C H sing 1.09 N N
73 C28 H282 C H sing 1.09 N N
74 C29 C30 C C sing 1.53 N N
75 C29 H291 C H sing 1.09 N N
76 C29 H292 C H sing 1.09 N N
77 C30 H301 C H sing 1.09 N N
78 C30 H302 C H sing 1.09 N N
79 C30 H303 C H sing 1.09 N N
80 C31 C32 C C sing 1.53 N N
81 C31 H311 C H sing 1.09 N N
82 C31 H312 C H sing 1.09 N N
83 C32 H321 C H sing 1.09 N N
84 C32 H322 C H sing 1.09 N N
85 C32 H323 C H sing 1.09 N N



R6G : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
R6G 2v3l Open in New Window Bound ligand 1 1