Chemical Components in the PDB

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BI3 : Summary

Code

BI3

One-letter code

X

Molecule name

3-[1-(3-AMINOPROPYL)-1H-INDOL-3-YL]-4-(1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE

Systematic names

ProgramVersionName
ACDLabs 10.04 3-[1-(3-aminopropyl)-1H-indol-3-yl]-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione
OpenEye OEToolkits 1.5.0 3-[1-(3-aminopropyl)indol-3-yl]-4-(1H-indol-3-yl)pyrrole-2,5-dione

Formula

C23 H20 N4 O2

Formal charge

0

Molecular weight

384.431 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C5C(c2c1ccccc1nc2)=C(c4c3ccccc3n(c4)CCCN)C(=O)N5
SMILES CACTVS 3.341 NCCCn1cc(c2ccccc12)C3=C(C(=O)NC3=O)c4c[nH]c5ccccc45
SMILES OpenEye OEToolkits 1.5.0 c1ccc2c(c1)c(c[nH]2)C3=C(C(=O)NC3=O)c4cn(c5c4cccc5)CCCN
Canonical SMILES CACTVS 3.341 NCCCn1cc(c2ccccc12)C3=C(C(=O)NC3=O)c4c[nH]c5ccccc45
Canonical SMILES OpenEye OEToolkits 1.5.0 c1ccc2c(c1)c(c[nH]2)C3=C(C(=O)NC3=O)c4cn(c5c4cccc5)CCCN

IUPAC InChI

InChI=1S/C23H20N4O2/c24-10-5-11-27-13-17(15-7-2-4-9-19(15)27)21-20(22(28)26-23(21)29)16-12-25-18-8-3-1-6-14(16)18/h1-4,6-9,12-13,25H,5,10-11,24H2,(H,26,28,29)

IUPAC InChI key

APYXQTXFRIDSGE-UHFFFAOYSA-N
BI3

wwPDB Information

Atom count

49 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2003-12-16

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



BI3 : Atoms of Molecule

Total Number of Atoms: 49
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 NBC N NBC N N N 0 1.788 2.107 6.512
2 CBB C CBB N N N 0 2.288 1.31 5.384
3 CBA C CBA N N N 0 1.143 1.036 4.406
4 CAY C CAY N N N 0 1.664 0.205 3.232
5 NAH N NAH N Y N 0 0.569 -0.056 2.295
6 CAW C CAW N Y N 0 0.235 0.741 1.245
7 CAE C CAE N Y N 0 -0.268 -1.151 2.349
8 CAF C CAF N Y N 0 -0.356 -2.239 3.21
9 CAA C CAA N Y N 0 -1.327 -3.197 3.011
10 CAB C CAB N Y N 0 -2.224 -3.086 1.959
11 CAC C CAC N Y N 0 -2.156 -2.013 1.097
12 CAD C CAD N Y N 0 -1.18 -1.037 1.287
13 CAG C CAG N Y N 0 -0.827 0.205 0.58
14 CAI C CAI N N N 0 -1.492 0.761 -0.61
15 CAT C CAT N N N 0 -2.636 1.696 -0.634
16 OAZ O OAZ N N N 0 -3.199 2.152 0.34
17 NAU N NAU N N N 0 -2.944 1.965 -1.914
18 CAV C CAV N N N 0 -2.127 1.297 -2.746
19 OAX O OAX N N N 0 -2.166 1.335 -3.96
20 CAJ C CAJ N N N 0 -1.174 0.507 -1.939
21 CAK C CAK N Y N 0 -0.104 -0.37 -2.442
22 CAM C CAM N Y N 0 1.285 0.017 -2.743
23 CAP C CAP N Y N 0 1.995 1.211 -2.653
24 CAQ C CAQ N Y N 0 3.325 1.243 -3.015
25 CAR C CAR N Y N 0 3.957 0.091 -3.46
26 CAS C CAS N Y N 0 3.267 -1.098 -3.547
27 CAN C CAN N Y N 0 1.925 -1.151 -3.187
28 NAO N NAO N Y N 0 0.993 -2.168 -3.167
29 CAL C CAL N Y N 0 -0.206 -1.7 -2.725
30 HBC1 H 1HBC N N N 0 1.529 3.008 6.138
31 HBC2 H 2HBC N N N 0 2.572 2.263 7.127
32 HBB1 H 1HBB N N N 0 3.079 1.859 4.873
33 HBB2 H 2HBB N N N 0 2.683 0.364 5.755
34 HBA1 H 1HBA N N N 0 0.353 0.486 4.917
35 HBA2 H 2HBA N N N 0 0.748 1.981 4.036
36 HAY1 H 1HAY N N N 0 2.455 0.755 2.721
37 HAY2 H 2HAY N N N 0 2.06 -0.739 3.602
38 HAW H HAW N N N 0 0.736 1.66 0.978
39 HAF H HAF N N N 0 0.336 -2.336 4.033
40 HAA H HAA N N N 0 -1.39 -4.043 3.68
41 HAB H HAB N N N 0 -2.98 -3.844 1.815
42 HAQ H HAQ N N N 0 3.877 2.169 -2.951
43 HAC H HAC N N N 0 -2.856 -1.929 0.279
44 HAU H HAU N N N 0 -3.659 2.555 -2.198
45 HAP H HAP N N N 0 1.506 2.11 -2.307
46 HAR H HAR N N N 0 4.999 0.127 -3.74
47 HAS H HAS N N N 0 3.769 -1.989 -3.895
48 HAO H HAO N N N 0 1.167 -3.085 -3.431
49 HAL H HAL N N N 0 -1.102 -2.293 -2.616



BI3 : Chemical Bonds

Total Number of Bonds: 53
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 NBC CBB N C sing 1.47 N N
2 NBC HBC1 N H sing 1.01 N N
3 NBC HBC2 N H sing 1.01 N N
4 CBB CBA C C sing 1.53 N N
5 CBB HBB1 C H sing 1.09 N N
6 CBB HBB2 C H sing 1.09 N N
7 CBA CAY C C sing 1.53 N N
8 CBA HBA1 C H sing 1.09 N N
9 CBA HBA2 C H sing 1.09 N N
10 CAY NAH C N sing 1.46 N N
11 CAY HAY1 C H sing 1.09 N N
12 CAY HAY2 C H sing 1.09 N N
13 NAH CAW N C sing 1.36 N Y
14 NAH CAE N C sing 1.38 N Y
15 CAW CAG C C doub 1.36 N Y
16 CAW HAW C H sing 1.08 N N
17 CAE CAF C C sing 1.39 N Y
18 CAE CAD C C doub 1.4 N Y
19 CAF CAA C C doub 1.38 N Y
20 CAF HAF C H sing 1.08 N N
21 CAA CAB C C sing 1.39 N Y
22 CAA HAA C H sing 1.08 N N
23 CAB CAC C C doub 1.38 N Y
24 CAB HAB C H sing 1.08 N N
25 CAC CAD C C sing 1.39 N Y
26 CAC HAC C H sing 1.08 N N
27 CAD CAG C C sing 1.47 N Y
28 CAG CAI C C sing 1.47 N N
29 CAI CAT C C sing 1.48 N N
30 CAI CAJ C C doub 1.39 N N
31 CAT OAZ C O doub 1.21 N N
32 CAT NAU C N sing 1.34 N N
33 NAU CAV N C sing 1.34 N N
34 NAU HAU N H sing 0.97 N N
35 CAV OAX C O doub 1.22 N N
36 CAV CAJ C C sing 1.48 N N
37 CAJ CAK C C sing 1.47 N N
38 CAK CAM C C sing 1.47 N Y
39 CAK CAL C C doub 1.36 N Y
40 CAM CAP C C sing 1.39 N Y
41 CAM CAN C C doub 1.4 N Y
42 CAP CAQ C C doub 1.38 N Y
43 CAP HAP C H sing 1.08 N N
44 CAQ CAR C C sing 1.39 N Y
45 CAQ HAQ C H sing 1.08 N N
46 CAR CAS C C doub 1.38 N Y
47 CAR HAR C H sing 1.08 N N
48 CAS CAN C C sing 1.39 N Y
49 CAS HAS C H sing 1.08 N N
50 CAN NAO C N sing 1.38 N Y
51 NAO CAL N C sing 1.36 N Y
52 NAO HAO N H sing 0.97 N N
53 CAL HAL C H sing 1.08 N N



BI3 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
BI3 1uu9 Open in New Window Bound ligand 1 1