Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

52E : Summary

Code

52E

One-letter code

X

Molecule name

4-{[(2-chloro-3-fluorobenzyl)carbamoyl](methyl)amino}-3,4-dideoxy-5-O-(isoquinolin-3-ylcarbamoyl)-D-erythro-pentitol

Systematic names

ProgramVersionName
ACDLabs 12.01 4-{[(2-chloro-3-fluorobenzyl)carbamoyl](methyl)amino}-3,4-dideoxy-5-O-(isoquinolin-3-ylcarbamoyl)-D-erythro-pentitol
OpenEye OEToolkits 1.9.2 [(2S,4R)-2-[(2-chloranyl-3-fluoranyl-phenyl)methylcarbamoyl-methyl-amino]-4,5-bis(oxidanyl)pentyl] N-isoquinolin-3-ylcarbamate

Formula

C24 H26 Cl F N4 O5

Formal charge

0

Molecular weight

504.938 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N(C(N(C(CC(CO)O)COC(Nc1ncc2c(c1)cccc2)=O)C)=O)Cc3c(c(ccc3)F)Cl
SMILES CACTVS 3.385 CN([CH](COC(=O)Nc1cc2ccccc2cn1)C[CH](O)CO)C(=O)NCc3cccc(F)c3Cl
SMILES OpenEye OEToolkits 1.9.2 CN(C(CC(CO)O)COC(=O)Nc1cc2ccccc2cn1)C(=O)NCc3cccc(c3Cl)F
Canonical SMILES CACTVS 3.385 CN([C@H](COC(=O)Nc1cc2ccccc2cn1)C[C@@H](O)CO)C(=O)NCc3cccc(F)c3Cl
Canonical SMILES OpenEye OEToolkits 1.9.2 CN([C@@H](C[C@H](CO)O)COC(=O)Nc1cc2ccccc2cn1)C(=O)NCc3cccc(c3Cl)F

IUPAC InChI

InChI=1S/C24H26ClFN4O5/c1-30(23(33)28-12-17-7-4-8-20(26)22(17)25)18(10-19(32)13-31)14-35-24(34)29-21-9-15-5-2-3-6-16(15)11-27-21/h2-9,11,18-19,31-32H,10,12-14H2,1H3,(H,28,33)(H,27,29,34)/t18-,19+/m0/s1

IUPAC InChI key

HLEXQOJKMXKUKE-RBUKOAKNSA-N
52E

wwPDB Information

Atom count

61 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-07-15

Last modified at

2016-11-11

Status

Released

Obsoleted

Not Assigned



52E : Atoms of Molecule

Total Number of Atoms: 61
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -3.043 0.383 0.854
2 C6 C C1 N Y N 0 -5.623 1.842 -0.244
3 N3 N N2 N N N 0 3.65 -0.471 -0.435
4 C5 C C2 N Y N 0 -6.17 2.936 -0.894
5 C15 C C3 N N N 0 -0.361 -3.288 0.011
6 C16 C C4 R N N 0 -1.746 -3.838 -0.334
7 C17 C C5 N N N 0 -1.606 -4.966 -1.359
8 O30 O O1 N N N 0 -2.885 -5.557 -1.594
9 O31 O O2 N N N 0 -2.55 -2.793 -0.883
10 N2 N N3 N N N 0 -1.251 -1.097 0.635
11 N4 N N4 N Y N 0 5.405 0.084 1.028
12 C7 C C6 N Y N 0 -5.92 4.214 -0.425
13 C8 C C7 N Y N 0 -5.125 4.398 0.691
14 C9 C C8 N Y N 0 -4.579 3.305 1.339
15 C10 C C9 N Y N 0 -4.827 2.028 0.872
16 C11 C C10 N N N 0 -4.231 0.838 1.58
17 C12 C C11 N N N 0 -2.341 -0.675 1.306
18 C13 C C12 N N N 0 -0.829 -0.405 -0.586
19 C14 C C13 S N N 0 -0.489 -2.247 1.126
20 C18 C C14 N N N 0 0.905 -1.788 1.557
21 C19 C C15 N N N 0 2.905 -0.901 0.603
22 C20 C C16 N Y N 0 4.91 0.083 -0.207
23 C21 C C17 N Y N 0 5.614 0.615 -1.267
24 C25 C C21 N Y N 0 7.662 1.73 -2.042
25 C22 C C18 N Y N 0 6.881 1.169 -1.021
26 C23 C C19 N Y N 0 7.376 1.153 0.31
27 C24 C C20 N Y N 0 6.582 0.587 1.32
28 C26 C C22 N Y N 0 8.884 2.251 -1.743
29 C27 C C23 N Y N 0 9.371 2.236 -0.437
30 C28 C C24 N Y N 0 8.641 1.7 0.58
31 O29 O O3 N N N 0 -2.692 -1.249 2.319
32 O32 O O4 N N N 0 1.649 -1.34 0.394
33 O33 O O5 N N N 0 3.366 -0.892 1.727
34 CL1 CL CL1 N N N 0 -5.94 0.237 -0.826
35 F35 F F1 N N N 0 -6.947 2.756 -1.984
36 H1 H H1 N N N 0 -2.763 0.841 0.046
37 H2 H H2 N N N 0 3.309 -0.546 -1.34
38 H3 H H3 N N N 0 0.28 -4.103 0.347
39 H4 H H4 N N N 0 0.076 -2.822 -0.872
40 H5 H H5 N N N 0 -2.219 -4.224 0.569
41 H6 H H6 N N N 0 -1.215 -4.562 -2.293
42 H7 H H7 N N N 0 -0.921 -5.722 -0.975
43 H8 H H8 N N N 0 -2.872 -6.281 -2.235
44 H9 H H9 N N N 0 -2.189 -2.401 -1.691
45 H10 H H10 N N N 0 -6.346 5.068 -0.931
46 H11 H H11 N N N 0 -4.93 5.395 1.057
47 H12 H H12 N N N 0 -3.958 3.45 2.21
48 H13 H H13 N N N 0 -4.965 0.033 1.617
49 H14 H H14 N N N 0 -3.951 1.122 2.594
50 H15 H H15 N N N 0 -1.248 -0.913 -1.454
51 H16 H H16 N N N 0 -1.183 0.625 -0.56
52 H17 H H17 N N N 0 0.259 -0.414 -0.65
53 H18 H H18 N N N 0 -1.006 -2.689 1.978
54 H19 H H19 N N N 0 0.814 -0.967 2.269
55 H20 H H20 N N N 0 1.432 -2.619 2.027
56 H21 H H21 N N N 0 5.2 0.607 -2.264
57 H22 H H22 N N N 0 6.94 0.565 2.339
58 H23 H H23 N N N 0 7.297 1.748 -3.059
59 H24 H H24 N N N 0 9.485 2.683 -2.53
60 H25 H H25 N N N 0 10.344 2.656 -0.228
61 H26 H H26 N N N 0 9.032 1.695 1.586



52E : Chemical Bonds

Total Number of Bonds: 63
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 F35 C5 F C sing 1.35 N N
2 C5 C7 C C doub 1.38 N Y
3 C5 C6 C C sing 1.39 N Y
4 CL1 C6 CL C sing 1.74 N N
5 C7 C8 C C sing 1.38 N Y
6 C6 C10 C C doub 1.38 N Y
7 C8 C9 C C doub 1.38 N Y
8 C10 C9 C C sing 1.38 N Y
9 C10 C11 C C sing 1.51 N N
10 C11 N1 C N sing 1.46 N N
11 C27 C26 C C doub 1.39 N Y
12 C27 C28 C C sing 1.36 N Y
13 C26 C25 C C sing 1.36 N Y
14 N1 C12 N C sing 1.35 N N
15 C28 C23 C C doub 1.4 N Y
16 C25 C22 C C doub 1.4 N Y
17 C23 C22 C C sing 1.42 N Y
18 C23 C24 C C sing 1.4 N Y
19 C22 C21 C C sing 1.4 N Y
20 C13 N2 C N sing 1.47 N N
21 C24 N4 C N doub 1.31 N Y
22 C21 C20 C C doub 1.38 N Y
23 C12 N2 C N sing 1.35 N N
24 C12 O29 C O doub 1.22 N N
25 N4 C20 N C sing 1.33 N Y
26 C20 N3 C N sing 1.4 N N
27 N2 C14 N C sing 1.46 N N
28 N3 C19 N C sing 1.35 N N
29 O32 C19 O C sing 1.35 N N
30 O32 C18 O C sing 1.45 N N
31 C19 O33 C O doub 1.21 N N
32 C14 C18 C C sing 1.53 N N
33 C14 C15 C C sing 1.53 N N
34 C15 C16 C C sing 1.53 N N
35 O31 C16 O C sing 1.43 N N
36 C16 C17 C C sing 1.53 N N
37 C17 O30 C O sing 1.43 N N
38 N1 H1 N H sing 0.97 N N
39 N3 H2 N H sing 0.97 N N
40 C15 H3 C H sing 1.09 N N
41 C15 H4 C H sing 1.09 N N
42 C16 H5 C H sing 1.09 N N
43 C17 H6 C H sing 1.09 N N
44 C17 H7 C H sing 1.09 N N
45 O30 H8 O H sing 0.97 N N
46 O31 H9 O H sing 0.97 N N
47 C7 H10 C H sing 1.08 N N
48 C8 H11 C H sing 1.08 N N
49 C9 H12 C H sing 1.08 N N
50 C11 H13 C H sing 1.09 N N
51 C11 H14 C H sing 1.09 N N
52 C13 H15 C H sing 1.09 N N
53 C13 H16 C H sing 1.09 N N
54 C13 H17 C H sing 1.09 N N
55 C14 H18 C H sing 1.09 N N
56 C18 H19 C H sing 1.09 N N
57 C18 H20 C H sing 1.09 N N
58 C21 H21 C H sing 1.08 N N
59 C24 H22 C H sing 1.08 N N
60 C25 H23 C H sing 1.08 N N
61 C26 H24 C H sing 1.08 N N
62 C27 H25 C H sing 1.08 N N
63 C28 H26 C H sing 1.08 N N



52E : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
52E 5m05 Open in New Window Bound ligand 1 1
52E 5t45 Open in New Window Bound ligand 1 1