Chemical Components in the PDB

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GOI : Summary

Code

GOI

One-letter code

X

Molecule name

2-{4-[3-(5H-dibenzo[b,f]azepin-5-yl)propyl]piperazin-1-yl}ethyl beta-D-glucopyranoside

Systematic names

ProgramVersionName
ACDLabs 12.01 2-{4-[3-(5H-dibenzo[b,f]azepin-5-yl)propyl]piperazin-1-yl}ethyl beta-D-glucopyranoside
OpenEye OEToolkits 1.7.2 (2R,3R,4S,5S,6R)-2-[2-[4-(3-benzo[b][1]benzazepin-11-ylpropyl)piperazin-1-yl]ethoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

Formula

C29 H39 N3 O6

Formal charge

0

Molecular weight

525.636 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O(CCN4CCN(CCCN3c1ccccc1C=Cc2ccccc23)CC4)C5OC(C(O)C(O)C5O)CO
SMILES CACTVS 3.370 OC[CH]1O[CH](OCCN2CCN(CCCN3c4ccccc4C=Cc5ccccc35)CC2)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.7.2 c1ccc2c(c1)C=Cc3ccccc3N2CCCN4CCN(CC4)CCOC5C(C(C(C(O5)CO)O)O)O
Canonical SMILES CACTVS 3.370 OC[C@H]1O[C@@H](OCCN2CCN(CCCN3c4ccccc4C=Cc5ccccc35)CC2)[C@H](O)[C@@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.7.2 c1ccc2c(c1)C=Cc3ccccc3N2CCCN4CCN(CC4)CCO[C@H]5[C@@H]([C@H]([C@@H]([C@H](O5)CO)O)O)O

IUPAC InChI

InChI=1S/C29H39N3O6/c33-20-25-26(34)27(35)28(36)29(38-25)37-19-18-31-16-14-30(15-17-31)12-5-13-32-23-8-3-1-6-21(23)10-11-22-7-2-4-9-24(22)32/h1-4,6-11,25-29,33-36H,5,12-20H2/t25-,26-,27+,28-,29-/m1/s1

IUPAC InChI key

GVUGRCGKZRTSLY-XYPQWYOHSA-N
GOI

wwPDB Information

Atom count

77 (38 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-10-20

Last modified at

2012-06-29

Status

Released

Obsoleted

Not Assigned



GOI : Atoms of Molecule

Total Number of Atoms: 77
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 R N N 0 -5.759 0.109 0.115
2 O1 O O1 N N N 0 -4.583 -0.421 -0.5
3 C2 C C2 R N N 0 -5.984 1.545 -0.367
4 O2 O O2 N N N 0 -4.884 2.362 0.038
5 C3 C C3 S N N 0 -7.277 2.086 0.249
6 O3 O O3 N N N 0 -7.534 3.399 -0.252
7 C4 C C4 S N N 0 -8.436 1.158 -0.128
8 O4 O O4 N N N 0 -9.636 1.612 0.501
9 C5 C C5 R N N 0 -8.117 -0.263 0.344
10 O5 O O5 N N N 0 -6.887 -0.693 -0.241
11 C6 C C6 N N N 0 -9.243 -1.207 -0.082
12 O6 O O6 N N N 0 -9.003 -2.509 0.458
13 CAE C CAE N Y N 0 8.541 3.281 -0.242
14 CAF C CAF N Y N 0 6.885 -3.479 -0.115
15 CAG C CAG N Y N 0 7.962 3.09 -1.408
16 CAH C CAH N Y N 0 6.45 -3.083 -1.293
17 CAI C CAI N Y N 0 8.112 2.497 0.927
18 CAJ C CAJ N Y N 0 6.877 -2.545 1.021
19 CAK C CAK N Y N 0 6.89 2.091 -1.539
20 CAL C CAL N Y N 0 5.959 -1.707 -1.468
21 CAM C CAM N N N 0 6.737 0.845 1.997
22 CAN C CAN N N N 0 6.431 -0.408 2.021
23 CAO C CAO N N N 0 3.182 -0.178 -0.176
24 CAQ C CAQ N N N 0 -4.218 -1.721 -0.032
25 CAR C CAR N N N 0 1.981 0.133 0.72
26 CAS C CAS N N N 0 -2.953 -2.187 -0.755
27 CAT C CAT N N N 0 -0.229 -0.641 1.337
28 CAU C CAU N N N 0 0.371 -0.433 -0.999
29 CAV C CAV N N N 0 -1.343 -1.622 0.964
30 CAW C CAW N N N 0 -0.743 -1.414 -1.372
31 CAX C CAX N N N 0 4.352 0.732 0.206
32 CBA C CBA N Y N 0 7.148 1.602 0.811
33 CBB C CBB N Y N 0 6.435 -1.31 0.866
34 CBC C CBC N Y N 0 6.507 1.384 -0.492
35 CBD C CBD N Y N 0 5.956 -0.867 -0.45
36 NBJ N NBJ N N N 0 0.858 -0.74 0.353
37 NBK N NBK N N N 0 -1.83 -1.314 -0.389
38 NBL N NBL N N N 0 5.505 0.433 -0.654
39 H1 H H1 N N N 0 -5.636 0.104 1.198
40 H2 H H2 N N N 0 -6.064 1.556 -1.454
41 HO2 H HO2 N N N 0 -4.03 2.074 -0.312
42 H3 H H3 N N N 0 -7.177 2.123 1.334
43 HO3 H HO3 N N N 0 -6.835 4.038 -0.055
44 H4 H H4 N N N 0 -8.569 1.162 -1.21
45 HO4 H HO4 N N N 0 -9.896 2.509 0.251
46 H5 H H5 N N N 0 -8.026 -0.273 1.431
47 H6 H H6 N N N 0 -10.195 -0.829 0.291
48 H6A H H6A N N N 0 -9.276 -1.266 -1.17
49 HO6 H HO6 N N N 0 -9.679 -3.161 0.228
50 HAE H HAE N N N 0 9.334 4.008 -0.144
51 HAF H HAF N N N 0 7.248 -4.487 0.016
52 HAG H HAG N N N 0 8.273 3.666 -2.267
53 HAH H HAH N N N 0 6.452 -3.767 -2.128
54 HAI H HAI N N N 0 8.587 2.655 1.884
55 HAJ H HAJ N N N 0 7.233 -2.87 1.988
56 HAK H HAK N N N 0 6.413 1.936 -2.496
57 HAL H HAL N N N 0 5.601 -1.383 -2.434
58 HAM H HAM N N N 0 6.687 1.383 2.933
59 HAN H HAN N N N 0 6.146 -0.829 2.974
60 HAO H HAO N N N 0 3.474 -1.22 -0.044
61 HAOA H HAOA N N N 0 2.913 -0.005 -1.218
62 HAQ H HAQ N N N 0 -4.03 -1.681 1.041
63 HAQA H HAQA N N N 0 -5.03 -2.421 -0.232
64 HAR H HAR N N N 0 2.25 -0.039 1.762
65 HARA H HARA N N N 0 1.689 1.175 0.587
66 HAS H HAS N N N 0 -2.726 -3.213 -0.464
67 HASA H HASA N N N 0 -3.112 -2.142 -1.832
68 HAT H HAT N N N 0 -0.625 0.375 1.34
69 HATA H HATA N N N 0 0.154 -0.885 2.328
70 HAU H HAU N N N 0 1.191 -0.525 -1.711
71 HAUA H HAUA N N N 0 -0.018 0.585 -1.022
72 HAV H HAV N N N 0 -0.954 -2.64 0.987
73 HAVA H HAVA N N N 0 -2.163 -1.529 1.675
74 HAW H HAW N N N 0 -1.125 -1.169 -2.363
75 HAWA H HAWA N N N 0 -0.347 -2.429 -1.375
76 HAX H HAX N N N 0 4.06 1.773 0.073
77 HAXA H HAXA N N N 0 4.621 0.559 1.248



GOI : Chemical Bonds

Total Number of Bonds: 81
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 O1 C O sing 1.43 N N
2 C1 C2 C C sing 1.53 N N
3 C1 O5 C O sing 1.43 N N
4 O1 CAQ O C sing 1.43 N N
5 C2 O2 C O sing 1.43 N N
6 C2 C3 C C sing 1.53 N N
7 C3 O3 C O sing 1.43 N N
8 C3 C4 C C sing 1.53 N N
9 C4 O4 C O sing 1.43 N N
10 C4 C5 C C sing 1.53 N N
11 C5 O5 C O sing 1.43 N N
12 C5 C6 C C sing 1.53 N N
13 C6 O6 C O sing 1.43 N N
14 CAE CAG C C doub 1.32 N Y
15 CAE CAI C C sing 1.47 N Y
16 CAF CAH C C doub 1.32 N Y
17 CAF CAJ C C sing 1.47 N Y
18 CAG CAK C C sing 1.47 N Y
19 CAH CAL C C sing 1.47 N Y
20 CAI CBA C C doub 1.32 N Y
21 CAJ CBB C C doub 1.32 N Y
22 CAK CBC C C doub 1.32 N Y
23 CAL CBD C C doub 1.32 N Y
24 CAM CAN C C doub 1.29 N N
25 CAM CBA C C sing 1.47 N N
26 CAN CBB C C sing 1.47 N N
27 CAO CAR C C sing 1.53 N N
28 CAO CAX C C sing 1.53 N N
29 CAQ CAS C C sing 1.53 N N
30 CAR NBJ C N sing 1.47 N N
31 CAS NBK C N sing 1.47 N N
32 CAT CAV C C sing 1.53 N N
33 CAT NBJ C N sing 1.47 N N
34 CAU CAW C C sing 1.53 N N
35 CAU NBJ C N sing 1.47 N N
36 CAV NBK C N sing 1.47 N N
37 CAW NBK C N sing 1.47 N N
38 CAX NBL C N sing 1.47 N N
39 CBA CBC C C sing 1.47 N Y
40 CBB CBD C C sing 1.47 N Y
41 CBC NBL C N sing 1.39 N N
42 CBD NBL C N sing 1.39 N N
43 C1 H1 C H sing 1.09 N N
44 C2 H2 C H sing 1.09 N N
45 O2 HO2 O H sing 0.97 N N
46 C3 H3 C H sing 1.09 N N
47 O3 HO3 O H sing 0.97 N N
48 C4 H4 C H sing 1.09 N N
49 O4 HO4 O H sing 0.97 N N
50 C5 H5 C H sing 1.09 N N
51 C6 H6 C H sing 1.09 N N
52 C6 H6A C H sing 1.09 N N
53 O6 HO6 O H sing 0.97 N N
54 CAE HAE C H sing 1.08 N N
55 CAF HAF C H sing 1.08 N N
56 CAG HAG C H sing 1.08 N N
57 CAH HAH C H sing 1.08 N N
58 CAI HAI C H sing 1.08 N N
59 CAJ HAJ C H sing 1.08 N N
60 CAK HAK C H sing 1.08 N N
61 CAL HAL C H sing 1.08 N N
62 CAM HAM C H sing 1.08 N N
63 CAN HAN C H sing 1.08 N N
64 CAO HAO C H sing 1.09 N N
65 CAO HAOA C H sing 1.09 N N
66 CAQ HAQ C H sing 1.09 N N
67 CAQ HAQA C H sing 1.09 N N
68 CAR HAR C H sing 1.09 N N
69 CAR HARA C H sing 1.09 N N
70 CAS HAS C H sing 1.09 N N
71 CAS HASA C H sing 1.09 N N
72 CAT HAT C H sing 1.09 N N
73 CAT HATA C H sing 1.09 N N
74 CAU HAU C H sing 1.09 N N
75 CAU HAUA C H sing 1.09 N N
76 CAV HAV C H sing 1.09 N N
77 CAV HAVA C H sing 1.09 N N
78 CAW HAW C H sing 1.09 N N
79 CAW HAWA C H sing 1.09 N N
80 CAX HAX C H sing 1.09 N N
81 CAX HAXA C H sing 1.09 N N



GOI : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
GOI 3vip Open in New Window Bound ligand 1 1