Chemical Components in the PDB

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BBB : Summary

Code

BBB

One-letter code

X

Molecule name

1-((2-HYDROXYETHOXY)METHYL)-5-(3-(BENZYLOXY)BENZYL)-6-HYDROXYPYRIMIDINE-2,4(1H,3H)-DIONE

Systematic names

ProgramVersionName
ACDLabs 10.04 5-[3-(benzyloxy)benzyl]-6-hydroxy-1-[(2-hydroxyethoxy)methyl]pyrimidine-2,4(1H,3H)-dione
OpenEye OEToolkits 1.5.0 6-hydroxy-1-(2-hydroxyethoxymethyl)-5-[(3-phenylmethoxyphenyl)methyl]pyrimidine-2,4-dione

Formula

C21 H22 N2 O6

Formal charge

0

Molecular weight

398.409 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1C(=C(O)N(C(=O)N1)COCCO)Cc3cccc(OCc2ccccc2)c3
SMILES CACTVS 3.341 OCCOCN1C(=O)NC(=O)C(=C1O)Cc2cccc(OCc3ccccc3)c2
SMILES OpenEye OEToolkits 1.5.0 c1ccc(cc1)COc2cccc(c2)CC3=C(N(C(=O)NC3=O)COCCO)O
Canonical SMILES CACTVS 3.341 OCCOCN1C(=O)NC(=O)C(=C1O)Cc2cccc(OCc3ccccc3)c2
Canonical SMILES OpenEye OEToolkits 1.5.0 c1ccc(cc1)COc2cccc(c2)CC3=C(N(C(=O)NC3=O)COCCO)O

IUPAC InChI

InChI=1S/C21H22N2O6/c24-9-10-28-14-23-20(26)18(19(25)22-21(23)27)12-16-7-4-8-17(11-16)29-13-15-5-2-1-3-6-15/h1-8,11,24,26H,9-10,12-14H2,(H,22,25,27)

IUPAC InChI key

CAWXCABXSPTFRN-UHFFFAOYSA-N
BBB

wwPDB Information

Atom count

51 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2004-08-10

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



BBB : Atoms of Molecule

Total Number of Atoms: 51
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OAC O OAC N N N 0 7.586 1.408 1.987
2 CAN C CAN N N N 0 7.441 2.36 3.034
3 CAO C CAO N N N 0 6.123 3.09 2.859
4 OAT O OAT N N N 0 5.062 2.145 2.891
5 CAR C CAR N N N 0 3.8 2.774 2.731
6 NBC N NBC N Y N 0 2.754 1.753 2.808
7 CBB C CBB N Y N 0 2.199 1.444 4.058
8 OAB O OAB N N N 0 2.527 1.977 5.12
9 NAS N NAS N Y N 0 1.216 0.458 4.03
10 CBA C CBA N Y N 0 0.755 -0.22 2.918
11 OAA O OAA N N N 0 -0.112 -1.089 2.976
12 CAY C CAY N Y N 0 2.345 1.12 1.636
13 CAZ C CAZ N Y N 0 1.387 0.172 1.623
14 CAQ C CAQ N N N 0 0.856 -0.548 0.416
15 CAW C CAW N Y N 0 1.367 -1.957 0.321
16 CAK C CAK N Y N 0 0.486 -2.988 0.015
17 CAH C CAH N Y N 0 0.961 -4.296 -0.072
18 CAL C CAL N Y N 0 2.312 -4.564 0.147
19 CAM C CAM N Y N 0 2.714 -2.215 0.541
20 CAX C CAX N Y N 0 3.189 -3.524 0.454
21 OAU O OAU N N N 0 4.507 -3.785 0.667
22 CAP C CAP N N N 0 5.348 -2.675 0.976
23 CAV C CAV N Y N 0 6.758 -3.16 1.143
24 CAJ C CAJ N Y N 0 7.205 -3.559 2.398
25 CAG C CAG N Y N 0 8.516 -4.01 2.553
26 CAE C CAE N Y N 0 9.371 -4.059 1.452
27 CAF C CAF N Y N 0 8.916 -3.657 0.197
28 CAI C CAI N Y N 0 7.605 -3.206 0.041
29 OAD O OAD N N N 0 3.002 1.537 0.491
30 HAC H HAC N N N 0 6.989 0.671 2.195
31 HAN1 H 1HAN N N N 0 7.472 1.825 3.988
32 HAN2 H 2HAN N N N 0 8.278 3.062 2.977
33 HAO1 H 1HAO N N N 0 6.086 3.612 1.898
34 HAO2 H 2HAO N N N 0 5.97 3.804 3.673
35 HAR1 H 1HAR N N N 0 3.624 3.5 3.531
36 HAR2 H 2HAR N N N 0 3.728 3.259 1.753
37 HAS H HAS N N N 0 0.794 0.211 4.921
38 HAQ1 H 1HAQ N N N 0 1.136 0.011 -0.481
39 HAQ2 H 2HAQ N N N 0 -0.236 -0.538 0.455
40 HAK H HAK N N N 0 -0.568 -2.788 -0.157
41 HAH H HAH N N N 0 0.278 -5.106 -0.312
42 HAL H HAL N N N 0 2.676 -5.586 0.076
43 HAM H HAM N N N 0 3.4 -1.406 0.781
44 HAP1 H 1HAP N N N 0 4.987 -2.198 1.893
45 HAP2 H 2HAP N N N 0 5.284 -1.94 0.167
46 HAJ H HAJ N N N 0 6.545 -3.524 3.261
47 HAG H HAG N N N 0 8.87 -4.323 3.531
48 HAE H HAE N N N 0 10.392 -4.41 1.573
49 HAF H HAF N N N 0 9.582 -3.695 -0.66
50 HAI H HAI N N N 0 7.259 -2.895 -0.941
51 HAD H HAD N N N 0 2.866 0.894 -0.21



BBB : 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 OAC CAN O C sing 1.42 N N
2 OAC HAC O H sing 0.97 N N
3 CAN CAO C C sing 1.52 N N
4 CAN HAN1 C H sing 1.09 N N
5 CAN HAN2 C H sing 1.09 N N
6 CAO OAT C O sing 1.42 N N
7 CAO HAO1 C H sing 1.09 N N
8 CAO HAO2 C H sing 1.09 N N
9 OAT CAR O C sing 1.42 N N
10 CAR NBC C N sing 1.46 N N
11 CAR HAR1 C H sing 1.09 N N
12 CAR HAR2 C H sing 1.09 N N
13 NBC CBB N C sing 1.4 N Y
14 NBC CAY N C sing 1.39 N Y
15 CBB OAB C O doub 1.23 N N
16 CBB NAS C N sing 1.39 N Y
17 NAS CBA N C sing 1.38 N Y
18 NAS HAS N H sing 1.02 N N
19 CBA OAA C O doub 1.23 N N
20 CBA CAZ C C sing 1.49 N Y
21 CAY CAZ C C doub 1.35 N Y
22 CAY OAD C O sing 1.38 N N
23 CAZ CAQ C C sing 1.5 N N
24 CAQ CAW C C sing 1.5 N N
25 CAQ HAQ1 C H sing 1.09 N N
26 CAQ HAQ2 C H sing 1.09 N N
27 CAW CAK C C doub 1.39 N Y
28 CAW CAM C C sing 1.39 N Y
29 CAK CAH C C sing 1.39 N Y
30 CAK HAK C H sing 1.09 N N
31 CAH CAL C C doub 1.39 N Y
32 CAH HAH C H sing 1.09 N N
33 CAL CAX C C sing 1.39 N Y
34 CAL HAL C H sing 1.09 N N
35 CAM CAX C C doub 1.4 N Y
36 CAM HAM C H sing 1.09 N N
37 CAX OAU C O sing 1.36 N N
38 OAU CAP O C sing 1.43 N N
39 CAP CAV C C sing 1.5 N N
40 CAP HAP1 C H sing 1.09 N N
41 CAP HAP2 C H sing 1.09 N N
42 CAV CAJ C C doub 1.39 N Y
43 CAV CAI C C sing 1.39 N Y
44 CAJ CAG C C sing 1.4 N Y
45 CAJ HAJ C H sing 1.09 N N
46 CAG CAE C C doub 1.39 N Y
47 CAG HAG C H sing 1.09 N N
48 CAE CAF C C sing 1.39 N Y
49 CAE HAE C H sing 1.09 N N
50 CAF CAI C C doub 1.4 N Y
51 CAF HAF C H sing 1.09 N N
52 CAI HAI C H sing 1.09 N N
53 OAD HAD O H sing 0.96 N N



BBB : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
BBB 1u1g Open in New Window Bound ligand 6 1