Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

9T0 : Summary

Code

9T0

One-letter code

X

Molecule name

5-[(2R,3R)-2-[2,2-bis(chloranyl)ethanoylamino]-3-(4-nitrophenyl)-3-[oxidanyl-[[4-[2,2,2-tris(fluoranyl)ethanoylamino]phenyl]methyl]phosphoryl]oxy-propoxy]-5-oxidanylidene-pentanoic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 5-{[(2R,3R)-2-[(dichloroacetyl)amino]-3-{[(R)-hydroxy({4-[(trifluoroacetyl)amino]phenyl}methyl)phosphoryl]oxy}-3-(4-nitrophenyl)propyl]oxy}-5-oxopentanoic acid
OpenEye OEToolkits 2.0.6 5-[(2~{R},3~{R})-2-[2,2-bis(chloranyl)ethanoylamino]-3-(4-nitrophenyl)-3-[oxidanyl-[[4-[2,2,2-tris(fluoranyl)ethanoylamino]phenyl]methyl]phosphoryl]oxy-propoxy]-5-oxidanylidene-pentanoic acid

Formula

C25 H25 Cl2 F3 N3 O11 P

Formal charge

0

Molecular weight

702.354 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC(=O)CCCC(OCC(NC(C(Cl)Cl)=O)C(c1ccc([N+]([O-])=O)cc1)OP(Cc2ccc(cc2)NC(C(F)(F)F)=O)(O)=O)=O
SMILES CACTVS 3.385 OC(=O)CCCC(=O)OC[CH](NC(=O)C(Cl)Cl)[CH](O[P](O)(=O)Cc1ccc(NC(=O)C(F)(F)F)cc1)c2ccc(cc2)[N+]([O-])=O
SMILES OpenEye OEToolkits 2.0.6 c1cc(ccc1CP(=O)(O)OC(c2ccc(cc2)[N+](=O)[O-])C(COC(=O)CCCC(=O)O)NC(=O)C(Cl)Cl)NC(=O)C(F)(F)F
Canonical SMILES CACTVS 3.385 OC(=O)CCCC(=O)OC[C@@H](NC(=O)C(Cl)Cl)[C@H](O[P](O)(=O)Cc1ccc(NC(=O)C(F)(F)F)cc1)c2ccc(cc2)[N+]([O-])=O
Canonical SMILES OpenEye OEToolkits 2.0.6 c1cc(ccc1CP(=O)(O)O[C@H](c2ccc(cc2)[N+](=O)[O-])[C@@H](COC(=O)CCCC(=O)O)NC(=O)C(Cl)Cl)NC(=O)C(F)(F)F

IUPAC InChI

InChI=1S/C25H25Cl2F3N3O11P/c26-22(27)23(37)32-18(12-43-20(36)3-1-2-19(34)35)21(15-6-10-17(11-7-15)33(39)40)44-45(41,42)13-14-4-8-16(9-5-14)31-24(38)25(28,29)30/h4-11,18,21-22H,1-3,12-13H2,(H,31,38)(H,32,37)(H,34,35)(H,41,42)/t18-,21-/m1/s1

IUPAC InChI key

DNCOXYFMDXAPCJ-WIYYLYMNSA-N
9T0

wwPDB Information

Atom count

70 (45 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-07-21

Last modified at

2019-07-19

Status

Released

Obsoleted

Not Assigned



9T0 : 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 O10 O O1 N N N 0 -2.957 -9.75 -0.366
2 C25 C C1 N N N 0 -2.343 -8.558 -0.425
3 O11 O O2 N N N 0 -1.137 -8.499 -0.441
4 C24 C C2 N N N 0 -3.16 -7.292 -0.47
5 C23 C C3 N N N 0 -2.224 -6.083 -0.533
6 C22 C C4 N N N 0 -3.053 -4.798 -0.578
7 C21 C C5 N N N 0 -2.131 -3.608 -0.64
8 O9 O O3 N N N 0 -0.934 -3.77 -0.647
9 O5 O O4 N N N 0 -2.64 -2.367 -0.688
10 C12 C C6 N N N 0 -1.693 -1.268 -0.746
11 C11 C C7 R N N 0 -2.454 0.059 -0.794
12 N1 N N1 N N N 0 -3.188 0.247 0.46
13 C13 C C8 N N N 0 -4.45 -0.212 0.576
14 O6 O O5 N N N 0 -4.947 -0.857 -0.323
15 C14 C C9 N N N 0 -5.245 0.078 1.824
16 CL2 CL CL1 N N N 0 -5.283 1.857 2.113
17 CL1 CL CL2 N N N 0 -6.928 -0.535 1.62
18 C10 C C10 R N N 0 -1.462 1.209 -0.981
19 C15 C C11 N Y N 0 -2.208 2.519 -0.993
20 C16 C C12 N Y N 0 -2.586 3.087 -2.195
21 C17 C C13 N Y N 0 -3.27 4.288 -2.206
22 C18 C C14 N Y N 0 -3.576 4.921 -1.015
23 N2 N N2 N N N 1 -4.307 6.207 -1.028
24 O8 O O6 N N N 0 -4.577 6.765 0.022
25 O7 O O7 N N N -1 -4.641 6.709 -2.086
26 C19 C C15 N Y N 0 -3.198 4.352 0.186
27 C20 C C16 N Y N 0 -2.518 3.148 0.198
28 O4 O O8 N N N 0 -0.521 1.207 0.095
29 P93 P P1 N N N 0 1.064 1.039 -0.127
30 O2 O O9 N N N 0 1.371 -0.425 -0.725
31 O3 O O10 N N N 0 1.541 2.069 -1.077
32 C9 C C17 N N N 0 1.926 1.236 1.467
33 C8 C C18 N Y N 0 3.415 1.202 1.241
34 C7 C C19 N Y N 0 4.102 2.375 0.988
35 C6 C C20 N Y N 0 5.467 2.346 0.78
36 C5 C C21 N Y N 0 4.093 -0.003 1.293
37 C4 C C22 N Y N 0 5.458 -0.038 1.086
38 C3 C C23 N Y N 0 6.15 1.138 0.826
39 N3 N N3 N N N 0 7.533 1.106 0.616
40 C2 C C24 N N N 0 8.099 0.04 0.015
41 O1 O O11 N N N 0 7.401 -0.848 -0.427
42 C1 C C25 N N N 0 9.598 -0.048 -0.107
43 F1 F F1 N N N 0 10.071 1.044 -0.841
44 F2 F F2 N N N 0 10.172 -0.036 1.169
45 F3 F F3 N N N 0 9.944 -1.235 -0.762
46 H1 H H1 N N N 0 -2.391 -10.534 -0.339
47 H2 H H2 N N N 0 -3.799 -7.303 -1.352
48 H3 H H3 N N N 0 -3.778 -7.227 0.426
49 H4 H H4 N N N 0 -1.585 -6.072 0.35
50 H5 H H5 N N N 0 -1.606 -6.149 -1.428
51 H6 H H6 N N N 0 -3.692 -4.809 -1.461
52 H7 H H7 N N N 0 -3.671 -4.733 0.317
53 H8 H H8 N N N 0 -1.056 -1.289 0.138
54 H9 H H9 N N N 0 -1.077 -1.366 -1.64
55 H10 H H10 N N N 0 -3.155 0.045 -1.628
56 H11 H H11 N N N 0 -2.766 0.701 1.206
57 H12 H H12 N N N 0 -4.778 -0.419 2.675
58 H13 H H13 N N N 0 -0.933 1.083 -1.926
59 H14 H H14 N N N 0 -2.347 2.593 -3.125
60 H15 H H15 N N N 0 -3.566 4.733 -3.145
61 H16 H H16 N N N 0 -3.437 4.846 1.116
62 H17 H H17 N N N 0 -2.223 2.704 1.137
63 H18 H H18 N N N 0 1.084 -1.151 -0.154
64 H19 H H19 N N N 0 1.648 2.191 1.914
65 H20 H H20 N N N 0 1.641 0.425 2.137
66 H21 H H21 N N N 0 3.57 3.314 0.952
67 H22 H H22 N N N 0 6.003 3.263 0.581
68 H23 H H23 N N N 0 3.555 -0.917 1.496
69 H24 H H24 N N N 0 5.987 -0.979 1.127
70 H25 H H25 N N N 0 8.085 1.85 0.902



9T0 : Chemical Bonds

Total Number of Bonds: 71
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O9 C21 O C doub 1.21 N N
2 O11 C25 O C doub 1.21 N N
3 C21 O5 C O sing 1.34 N N
4 C21 C22 C C sing 1.51 N N
5 O5 C12 O C sing 1.45 N N
6 C22 C23 C C sing 1.53 N N
7 C24 C25 C C sing 1.51 N N
8 C24 C23 C C sing 1.53 N N
9 C25 O10 C O sing 1.34 N N
10 O6 C13 O C doub 1.21 N N
11 C12 C11 C C sing 1.53 N N
12 CL1 C14 CL C sing 1.8 N N
13 C11 N1 C N sing 1.47 N N
14 C11 C10 C C sing 1.53 N N
15 C13 N1 C N sing 1.35 N N
16 C13 C14 C C sing 1.51 N N
17 C20 C19 C C doub 1.38 N Y
18 C20 C15 C C sing 1.38 N Y
19 C14 CL2 C CL sing 1.8 N N
20 C10 C15 C C sing 1.51 N N
21 C10 O4 C O sing 1.43 N N
22 C19 C18 C C sing 1.38 N Y
23 O3 P93 O P doub 1.48 N N
24 C15 C16 C C doub 1.38 N Y
25 O4 P93 O P sing 1.61 N N
26 O8 N2 O N doub 1.22 N N
27 O2 P93 O P sing 1.61 N N
28 P93 C9 P C sing 1.82 N N
29 C18 N2 C N sing 1.48 N N
30 C18 C17 C C doub 1.38 N Y
31 C16 C17 C C sing 1.38 N Y
32 N2 O7 N O sing 1.22 N N
33 C5 C4 C C doub 1.38 N Y
34 C5 C8 C C sing 1.38 N Y
35 C9 C8 C C sing 1.51 N N
36 C4 C3 C C sing 1.39 N Y
37 C8 C7 C C doub 1.38 N Y
38 C3 N3 C N sing 1.4 N N
39 C3 C6 C C doub 1.39 N Y
40 N3 C2 N C sing 1.35 N N
41 F2 C1 F C sing 1.4 N N
42 C7 C6 C C sing 1.38 N Y
43 C2 C1 C C sing 1.51 N N
44 C2 O1 C O doub 1.21 N N
45 C1 F3 C F sing 1.4 N N
46 C1 F1 C F sing 1.4 N N
47 O10 H1 O H sing 0.97 N N
48 C24 H2 C H sing 1.09 N N
49 C24 H3 C H sing 1.09 N N
50 C23 H4 C H sing 1.09 N N
51 C23 H5 C H sing 1.09 N N
52 C22 H6 C H sing 1.09 N N
53 C22 H7 C H sing 1.09 N N
54 C12 H8 C H sing 1.09 N N
55 C12 H9 C H sing 1.09 N N
56 C11 H10 C H sing 1.09 N N
57 N1 H11 N H sing 0.97 N N
58 C14 H12 C H sing 1.09 N N
59 C10 H13 C H sing 1.09 N N
60 C16 H14 C H sing 1.08 N N
61 C17 H15 C H sing 1.08 N N
62 C19 H16 C H sing 1.08 N N
63 C20 H17 C H sing 1.08 N N
64 O2 H18 O H sing 0.97 N N
65 C9 H19 C H sing 1.09 N N
66 C9 H20 C H sing 1.09 N N
67 C7 H21 C H sing 1.08 N N
68 C6 H22 C H sing 1.08 N N
69 C5 H23 C H sing 1.08 N N
70 C4 H24 C H sing 1.08 N N
71 N3 H25 N H sing 0.97 N N



9T0 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
9T0 6a9k Open in New Window Bound ligand 2 1