Chemical Components in the PDB

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X2P : Summary

Code

X2P

One-letter code

X

Molecule name

(1R,2R,5S)-8'-(3-chloro-4-fluorobenzyl)-6'-hydroxy-2'-[(2S)-2-hydroxypropyl]-9',10'-dihydro-2'H-spiro[bicyclo[3.1.0]hexane-2,3'-imidazo[5,1-a][2,6]naphthyridine]-1',5',7'(8'H)-trione

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R,2R,5S)-8'-(3-chloro-4-fluorobenzyl)-6'-hydroxy-2'-[(2S)-2-hydroxypropyl]-9',10'-dihydro-2'H-spiro[bicyclo[3.1.0]hexane-2,3'-imidazo[5,1-a][2,6]naphthyridine]-1',5',7'(8'H)-trione
OpenEye OEToolkits 1.9.2 (1'R,3R,5'S)-8-[(3-chloranyl-4-fluoranyl-phenyl)methyl]-6-oxidanyl-2-[(2S)-2-oxidanylpropyl]spiro[9,10-dihydroimidazo[5,1-a][2,6]naphthyridine-3,2'-bicyclo[3.1.0]hexane]-1,5,7-trione

Formula

C25 H25 Cl F N3 O5

Formal charge

0

Molecular weight

501.935 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N13C5(N(CC(C)O)C(C1=C4CCN(Cc2ccc(F)c(c2)Cl)C(C4=C(C3=O)O)=O)=O)CCC6CC56
SMILES CACTVS 3.385 C[CH](O)CN1C(=O)C2=C3CCN(Cc4ccc(F)c(Cl)c4)C(=O)C3=C(O)C(=O)N2[C]15CC[CH]6C[CH]56
SMILES OpenEye OEToolkits 1.9.2 CC(CN1C(=O)C2=C3CCN(C(=O)C3=C(C(=O)N2C14CCC5C4C5)O)Cc6ccc(c(c6)Cl)F)O
Canonical SMILES CACTVS 3.385 C[C@H](O)CN1C(=O)C2=C3CCN(Cc4ccc(F)c(Cl)c4)C(=O)C3=C(O)C(=O)N2[C@@]15CC[C@H]6C[C@@H]56
Canonical SMILES OpenEye OEToolkits 1.9.2 C[C@@H](CN1C(=O)C2=C3CCN(C(=O)C3=C(C(=O)N2[C@@]14CC[C@@H]5[C@H]4C5)O)Cc6ccc(c(c6)Cl)F)O

IUPAC InChI

InChI=1S/C25H25ClFN3O5/c1-12(31)10-29-23(34)20-15-5-7-28(11-13-2-3-18(27)17(26)8-13)22(33)19(15)21(32)24(35)30(20)25(29)6-4-14-9-16(14)25/h2-3,8,12,14,16,31-32H,4-7,9-11H2,1H3/t12-,14-,16+,25+/m0/s1

IUPAC InChI key

SUYSDXIXCVFTRC-UCVJIWRCSA-N
X2P

wwPDB Information

Atom count

60 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-05-14

Last modified at

2015-10-02

Status

Released

Obsoleted

Not Assigned



X2P : Atoms of Molecule

Total Number of Atoms: 60
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 -2.316 -1.028 -0.101
2 C4 C C1 N N N 0 -0.062 1.652 -1.486
3 C5 C C2 N N N 0 -1.849 0.184 -0.56
4 C6 C C3 N N N 0 -1.515 -2.11 -0.047
5 C7 C C4 N N N 0 -0.105 -1.989 -0.447
6 C8 C C5 R N N 0 -3.721 -0.835 0.252
7 C10 C C6 N N N 0 -5.379 1.172 0.143
8 C13 C C7 N N N 0 -3.956 -1.153 1.742
9 C15 C C8 R N N 0 -5.733 -2.24 0.468
10 C17 C C9 N N N 0 -6.077 -1.421 -0.778
11 C20 C C10 N Y N 0 4.879 2.179 -0.304
12 C21 C C11 N Y N 0 5.802 2.23 0.724
13 C22 C C12 N Y N 0 6.412 1.068 1.164
14 C24 C C13 N Y N 0 5.172 -0.194 -0.453
15 F F F1 N N N 0 7.314 1.117 2.168
16 C23 C C14 N Y N 0 6.095 -0.146 0.574
17 CL CL CL1 N N N 0 6.864 -1.603 1.12
18 C19 C C15 N Y N 0 4.56 0.967 -0.888
19 C18 C C16 N N N 0 3.553 0.914 -2.008
20 N N N2 N N N 0 2.214 0.707 -1.451
21 C1 C C17 N N N 0 1.756 -0.548 -1.277
22 O4 O O1 N N N 0 2.492 -1.5 -1.448
23 C2 C C18 N N N 0 0.349 -0.754 -0.874
24 O O O2 N N N 0 0.726 -3.056 -0.397
25 O1 O O3 N N N 0 -1.957 -3.181 0.331
26 C16 C C19 R N N 0 -4.622 -1.815 -0.512
27 C14 C C20 N N N 0 -5.47 -1.482 1.786
28 N2 N N3 N N N 0 -4.067 0.549 -0.046
29 C11 C C21 S N N 0 -5.269 2.29 1.181
30 O3 O O4 N N N 0 -4.427 3.328 0.676
31 C12 C C22 N N N 0 -6.66 2.857 1.471
32 C9 C C23 N N N 0 -2.962 1.154 -0.526
33 O2 O O5 N N N 0 -2.893 2.316 -0.877
34 C3 C C24 N N N 0 -0.552 0.331 -0.951
35 C C C25 N N N 0 1.398 1.865 -1.095
36 H1 H H1 N N N 0 -0.15 1.657 -2.573
37 H2 H H2 N N N 0 -0.667 2.458 -1.071
38 H3 H H3 N N N 0 -5.724 1.588 -0.804
39 H4 H H4 N N N 0 -6.09 0.422 0.49
40 H5 H H5 N N N 0 -3.364 -2.014 2.052
41 H6 H H6 N N N 0 -3.727 -0.287 2.363
42 H7 H H7 N N N 0 -6.065 -3.276 0.534
43 H8 H H8 N N N 0 -6.596 -1.933 -1.588
44 H9 H H9 N N N 0 -6.349 -0.375 -0.633
45 H10 H H10 N N N 0 4.404 3.086 -0.648
46 H11 H H11 N N N 0 6.049 3.176 1.182
47 H12 H H12 N N N 0 4.925 -1.139 -0.914
48 H13 H H13 N N N 0 3.575 1.852 -2.562
49 H14 H H14 N N N 0 3.799 0.09 -2.678
50 H15 H H15 N N N 0 0.305 -3.868 -0.083
51 H16 H H16 N N N 0 -4.142 -2.542 -1.166
52 H17 H H17 N N N 0 -5.697 -2.117 2.643
53 H18 H H18 N N N 0 -6.058 -0.565 1.823
54 H19 H H19 N N N 0 -4.841 1.891 2.101
55 H20 H H20 N N N 0 -4.748 3.73 -0.143
56 H21 H H21 N N N 0 -7.302 2.065 1.857
57 H22 H H22 N N N 0 -6.581 3.653 2.211
58 H23 H H23 N N N 0 -7.088 3.256 0.551
59 H24 H H24 N N N 0 1.781 2.745 -1.612
60 H25 H H25 N N N 0 1.46 2.029 -0.019



X2P : Chemical Bonds

Total Number of Bonds: 65
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O C7 O C sing 1.35 N N
2 O1 C6 O C doub 1.22 N N
3 C14 C15 C C sing 1.54 N N
4 C14 C13 C C sing 1.55 N N
5 C15 C17 C C sing 1.53 N N
6 C15 C16 C C sing 1.54 N N
7 C6 C7 C C sing 1.47 N N
8 C6 N1 C N sing 1.35 N N
9 C7 C2 C C doub 1.38 N N
10 O4 C1 O C doub 1.22 N N
11 CL C23 CL C sing 1.74 N N
12 C17 C16 C C sing 1.53 N N
13 C16 C8 C C sing 1.53 N N
14 C13 C8 C C sing 1.54 N N
15 N1 C8 N C sing 1.46 N N
16 N1 C5 N C sing 1.38 N N
17 C1 C2 C C sing 1.48 N N
18 C1 N C N sing 1.35 N N
19 C2 C3 C C sing 1.41 N N
20 C8 N2 C N sing 1.46 N N
21 C24 C23 C C doub 1.38 N Y
22 C24 C19 C C sing 1.38 N Y
23 C23 C22 C C sing 1.39 N Y
24 C5 C3 C C doub 1.36 N N
25 C5 C9 C C sing 1.48 N N
26 N C18 N C sing 1.46 N N
27 N C N C sing 1.46 N N
28 C3 C4 C C sing 1.51 N N
29 C18 C19 C C sing 1.51 N N
30 C19 C20 C C doub 1.38 N Y
31 N2 C9 N C sing 1.35 N N
32 N2 C10 N C sing 1.46 N N
33 C22 F C F sing 1.35 N N
34 C22 C21 C C doub 1.38 N Y
35 C9 O2 C O doub 1.22 N N
36 C C4 C C sing 1.53 N N
37 C10 C11 C C sing 1.53 N N
38 O3 C11 O C sing 1.43 N N
39 C20 C21 C C sing 1.38 N Y
40 C11 C12 C C sing 1.53 N N
41 C4 H1 C H sing 1.09 N N
42 C4 H2 C H sing 1.09 N N
43 C10 H3 C H sing 1.09 N N
44 C10 H4 C H sing 1.09 N N
45 C13 H5 C H sing 1.09 N N
46 C13 H6 C H sing 1.09 N N
47 C15 H7 C H sing 1.09 N N
48 C17 H8 C H sing 1.09 N N
49 C17 H9 C H sing 1.09 N N
50 C20 H10 C H sing 1.08 N N
51 C21 H11 C H sing 1.08 N N
52 C24 H12 C H sing 1.08 N N
53 C18 H13 C H sing 1.09 N N
54 C18 H14 C H sing 1.09 N N
55 O H15 O H sing 0.97 N N
56 C16 H16 C H sing 1.09 N N
57 C14 H17 C H sing 1.09 N N
58 C14 H18 C H sing 1.09 N N
59 C11 H19 C H sing 1.09 N N
60 O3 H20 O H sing 0.97 N N
61 C12 H21 C H sing 1.09 N N
62 C12 H22 C H sing 1.09 N N
63 C12 H23 C H sing 1.09 N N
64 C H24 C H sing 1.09 N N
65 C H25 C H sing 1.09 N N



X2P : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
X2P 4ztf Open in New Window Bound ligand 1 1