Chemical Components in the PDB

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Y2O : Summary

Code

Y2O

One-letter code

X

Molecule name

benzyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate

Systematic names

ProgramVersionName
ACDLabs 12.01 benzyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate
OpenEye OEToolkits 2.0.7 (phenylmethyl) (2~{R},3~{S})-2-(carbamimidamidomethyl)-3-[[2-[(4-chloranyl-3-fluoranyl-phenyl)amino]-2-oxidanylidene-ethanoyl]amino]-6-(methylaminomethyl)-2,3-dihydroindole-1-carboxylate

Formula

C28 H29 Cl F N7 O4

Formal charge

0

Molecular weight

582.026 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Clc1ccc(cc1F)NC(=O)C(=O)NC1c2ccc(cc2N(C1CNC(=N)N)C(=O)OCc1ccccc1)CNC
SMILES CACTVS 3.385 CNCc1ccc2[CH](NC(=O)C(=O)Nc3ccc(Cl)c(F)c3)[CH](CNC(N)=N)N(C(=O)OCc4ccccc4)c2c1
SMILES OpenEye OEToolkits 2.0.7 CNCc1ccc2c(c1)N(C(C2NC(=O)C(=O)Nc3ccc(c(c3)F)Cl)CNC(=N)N)C(=O)OCc4ccccc4
Canonical SMILES CACTVS 3.385 CNCc1ccc2[C@H](NC(=O)C(=O)Nc3ccc(Cl)c(F)c3)[C@@H](CNC(N)=N)N(C(=O)OCc4ccccc4)c2c1
Canonical SMILES OpenEye OEToolkits 2.0.7 [H]/N=C(/N)\NC[C@@H]1[C@H](c2ccc(cc2N1C(=O)OCc3ccccc3)CNC)NC(=O)C(=O)Nc4ccc(c(c4)F)Cl

IUPAC InChI

InChI=1S/C28H29ClFN7O4/c1-33-13-17-7-9-19-22(11-17)37(28(40)41-15-16-5-3-2-4-6-16)23(14-34-27(31)32)24(19)36-26(39)25(38)35-18-8-10-20(29)21(30)12-18/h2-12,23-24,33H,13-15H2,1H3,(H,35,38)(H,36,39)(H4,31,32,34)/t23-,24+/m1/s1

IUPAC InChI key

JMHDRQIIOQZAQE-RPWUZVMVSA-N
Y2O

wwPDB Information

Atom count

70 (41 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-12-27

Last modified at

2023-03-31

Status

Released

Obsoleted

Not Assigned



Y2O : Atoms of Molecule

Total Number of Atoms: 70
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N Y N 0 6.769 -1.333 -2.352
2 C13 C C2 N N N 0 1.484 3.207 0.401
3 C15 C C3 N N N 0 0.399 5.388 0.739
4 C20 C C4 N N N 0 -2.17 0.551 1.01
5 C21 C C5 N N N 0 -3.459 0.165 0.363
6 C24 C C6 N Y N 0 -6.07 -0.081 -0.772
7 C02 C C7 N N N 0 3.375 1.239 -1.001
8 C04 C C8 N N N 0 5.578 0.8 -1.808
9 C05 C C9 N Y N 0 6.705 -0.177 -1.596
10 C06 C C10 N Y N 0 7.675 0.082 -0.646
11 C07 C C11 N Y N 0 8.709 -0.815 -0.452
12 C08 C C12 N Y N 0 8.773 -1.97 -1.208
13 C09 C C13 N Y N 0 7.8 -2.232 -2.154
14 C12 C C14 R N N 0 1.114 1.815 -0.115
15 C18 C C15 S N N 0 0.202 1.097 0.893
16 C23 C C16 N Y N 0 -5.748 -0.46 0.524
17 C25 C C17 N Y N 0 -7.243 -0.532 -1.351
18 C27 C C18 N Y N 0 -8.092 -1.365 -0.639
19 C29 C C19 N Y N 0 -7.768 -1.747 0.651
20 C30 C C20 N Y N 0 -6.601 -1.295 1.235
21 C33 C C21 N Y N 0 2.186 -0.14 0.618
22 C34 C C22 N Y N 0 0.979 -0.135 1.299
23 C35 C C23 N Y N 0 0.666 -1.156 2.176
24 C36 C C24 N Y N 0 1.557 -2.193 2.382
25 C37 C C25 N Y N 0 2.764 -2.206 1.708
26 C38 C C26 N N N 0 3.737 -3.335 1.931
27 C40 C C27 N N N 0 4.398 -5.532 1.158
28 C41 C C28 N Y N 0 3.081 -1.19 0.832
29 F26 F F1 N N N 0 -7.561 -0.16 -2.61
30 N11 N N1 N N N 0 2.31 0.975 -0.217
31 N14 N N2 N N N 0 0.292 4.058 0.408
32 N16 N N3 N N N 0 1.562 5.892 1.047
33 N17 N N4 N N N 0 -0.719 6.188 0.745
34 N19 N N5 N N N 0 -1.063 0.718 0.259
35 N22 N N6 N N N 0 -4.566 -0.002 1.114
36 N39 N N7 N N N 0 3.467 -4.412 0.969
37 O01 O O1 N N N 0 3.346 2.181 -1.767
38 O03 O O2 N N N 0 4.469 0.458 -0.934
39 O31 O O3 N N N 0 -3.51 0.001 -0.838
40 O32 O O4 N N N 0 -2.118 0.715 2.211
41 CL28 CL CL1 N N N 0 -9.563 -1.93 -1.367
42 H1 H H1 N N N 0 6.011 -1.535 -3.094
43 H2 H H2 N N N 0 1.878 3.125 1.415
44 H3 H H3 N N N 0 2.241 3.646 -0.248
45 H4 H H4 N N N 0 -5.409 0.568 -1.327
46 H5 H H5 N N N 0 5.923 1.808 -1.578
47 H6 H H6 N N N 0 5.249 0.757 -2.846
48 H7 H H7 N N N 0 7.625 0.984 -0.055
49 H8 H H8 N N N 0 9.47 -0.61 0.287
50 H9 H H9 N N N 0 9.581 -2.671 -1.057
51 H10 H H10 N N N 0 7.85 -3.135 -2.744
52 H11 H H11 N N N 0 0.622 1.891 -1.085
53 H12 H H12 N N N 0 0.017 1.733 1.759
54 H13 H H13 N N N 0 -8.431 -2.396 1.204
55 H14 H H14 N N N 0 -6.35 -1.594 2.242
56 H15 H H15 N N N 0 -0.278 -1.144 2.702
57 H16 H H16 N N N 0 1.311 -2.99 3.068
58 H17 H H17 N N N 0 4.755 -2.97 1.793
59 H18 H H18 N N N 0 3.623 -3.717 2.946
60 H19 H H19 N N N 0 5.421 -5.183 1.014
61 H20 H H20 N N N 0 4.289 -5.93 2.167
62 H21 H H21 N N N 0 4.176 -6.315 0.433
63 H22 H H22 N N N 0 4.025 -1.206 0.308
64 H23 H H23 N N N 0 -0.573 3.684 0.179
65 H24 H H24 N N N 0 1.637 6.83 1.281
66 H25 H H25 N N N 0 -1.584 5.813 0.516
67 H26 H H26 N N N 0 -0.643 7.126 0.978
68 H27 H H27 N N N 0 -1.104 0.587 -0.701
69 H28 H H28 N N N 0 -4.543 0.197 2.063
70 H29 H H29 N N N 0 2.51 -4.723 1.034



Y2O : Chemical Bonds

Total Number of Bonds: 73
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C07 C08 C C doub 1.38 N Y
2 C07 C06 C C sing 1.38 N Y
3 C08 C09 C C sing 1.38 N Y
4 C06 C05 C C doub 1.38 N Y
5 N16 C15 N C doub 1.3 N N
6 C09 C10 C C doub 1.38 N Y
7 C05 C10 C C sing 1.38 N Y
8 C05 C04 C C sing 1.51 N N
9 C15 N14 C N sing 1.37 N N
10 C15 N17 C N sing 1.37 N N
11 N14 C13 N C sing 1.46 N N
12 C04 O03 C O sing 1.45 N N
13 O03 C02 O C sing 1.35 N N
14 C13 C12 C C sing 1.53 N N
15 C29 C30 C C doub 1.38 N Y
16 C29 C27 C C sing 1.38 N Y
17 C30 C23 C C sing 1.39 N Y
18 O32 C20 O C doub 1.21 N N
19 C12 N11 C N sing 1.47 N N
20 C12 C18 C C sing 1.54 N N
21 C27 CL28 C CL sing 1.74 N N
22 C27 C25 C C doub 1.39 N Y
23 C02 O01 C O doub 1.21 N N
24 C02 N11 C N sing 1.35 N N
25 N22 C23 N C sing 1.4 N N
26 N22 C21 N C sing 1.35 N N
27 C23 C24 C C doub 1.39 N Y
28 C20 C21 C C sing 1.49 N N
29 C20 N19 C N sing 1.35 N N
30 N11 C33 N C sing 1.4 N N
31 C21 O31 C O doub 1.21 N N
32 C18 N19 C N sing 1.46 N N
33 C18 C34 C C sing 1.51 N N
34 C25 C24 C C sing 1.38 N Y
35 C25 F26 C F sing 1.35 N N
36 C33 C34 C C doub 1.39 N Y
37 C33 C41 C C sing 1.4 N Y
38 C34 C35 C C sing 1.38 N Y
39 C41 C37 C C doub 1.38 N Y
40 C35 C36 C C doub 1.38 N Y
41 C37 C36 C C sing 1.38 N Y
42 C37 C38 C C sing 1.51 N N
43 C38 N39 C N sing 1.47 N N
44 N39 C40 N C sing 1.47 N N
45 C10 H1 C H sing 1.08 N N
46 C13 H2 C H sing 1.09 N N
47 C13 H3 C H sing 1.09 N N
48 C24 H4 C H sing 1.08 N N
49 C04 H5 C H sing 1.09 N N
50 C04 H6 C H sing 1.09 N N
51 C06 H7 C H sing 1.08 N N
52 C07 H8 C H sing 1.08 N N
53 C08 H9 C H sing 1.08 N N
54 C09 H10 C H sing 1.08 N N
55 C12 H11 C H sing 1.09 N N
56 C18 H12 C H sing 1.09 N N
57 C29 H13 C H sing 1.08 N N
58 C30 H14 C H sing 1.08 N N
59 C35 H15 C H sing 1.08 N N
60 C36 H16 C H sing 1.08 N N
61 C38 H17 C H sing 1.09 N N
62 C38 H18 C H sing 1.09 N N
63 C40 H19 C H sing 1.09 N N
64 C40 H20 C H sing 1.09 N N
65 C40 H21 C H sing 1.09 N N
66 C41 H22 C H sing 1.08 N N
67 N14 H23 N H sing 0.97 N N
68 N16 H24 N H sing 0.97 N N
69 N17 H25 N H sing 0.97 N N
70 N17 H26 N H sing 0.97 N N
71 N19 H27 N H sing 0.97 N N
72 N22 H28 N H sing 0.97 N N
73 N39 H29 N H sing 1.01 N N



Y2O : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
Y2O 8fm7 Open in New Window Bound ligand 4 1