Chemical Components in the PDB

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X6I : Summary

Code

X6I

One-letter code

X

Molecule name

S-{2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]ethyl}-L-cysteine

Systematic names

ProgramVersionName
ACDLabs 12.01 S-{2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]ethyl}-L-cysteine
OpenEye OEToolkits 2.0.7 (2~{R})-2-azanyl-3-[2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]ethylsulfanyl]propanoic acid

Formula

C13 H20 N3 O7 P S

Formal charge

0

Molecular weight

393.353 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Oc1c(/C=N/CCSCC(N)C(=O)O)c(cnc1C)COP(=O)(O)O
SMILES CACTVS 3.385 Cc1ncc(CO[P](O)(O)=O)c(C=NCCSC[CH](N)C(O)=O)c1O
SMILES OpenEye OEToolkits 2.0.7 Cc1c(c(c(cn1)COP(=O)(O)O)C=NCCSCC(C(=O)O)N)O
Canonical SMILES CACTVS 3.385 Cc1ncc(CO[P](O)(O)=O)c(C=NCCSC[C@H](N)C(O)=O)c1O
Canonical SMILES OpenEye OEToolkits 2.0.7 Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/CCSC[C@@H](C(=O)O)N)O

IUPAC InChI

InChI=1S/C13H20N3O7PS/c1-8-12(17)10(9(4-16-8)6-23-24(20,21)22)5-15-2-3-25-7-11(14)13(18)19/h4-5,11,17H,2-3,6-7,14H2,1H3,(H,18,19)(H2,20,21,22)/b15-5+/t11-/m0/s1

IUPAC InChI key

BWEPWNLQXWSAOF-QZSDQICDSA-N
X6I

wwPDB Information

Atom count

45 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-06-02

Last modified at

2024-06-28

Status

Released

Obsoleted

Not Assigned



X6I : Atoms of Molecule

Total Number of Atoms: 45
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -2.714 5.027 -0.749
2 C10 C C2 N N N 0 5.313 -0.343 -0.277
3 C11 C C3 R N N 0 6.576 -1.117 0.105
4 C12 C C4 N N N 0 7.586 -1.014 -1.009
5 C13 C C5 N Y N 0 -1.717 2.849 -0.024
6 C2 C C6 N Y N 0 -2.817 3.543 -0.507
7 C3 C C7 N Y N 0 -4.098 1.624 -0.563
8 C4 C C8 N Y N 0 -3.058 0.854 -0.086
9 C5 C C9 N N N 0 -3.24 -0.627 0.129
10 C6 C C10 N Y N 0 -1.831 1.467 0.195
11 C7 C C11 N N N 0 -0.69 0.682 0.707
12 C8 C C12 N N N 0 1.567 0.489 1.468
13 C9 C C13 N N N 0 2.696 0.496 0.435
14 N1 N N1 N Y N 0 -3.951 2.921 -0.756
15 N2 N N2 N N N 0 0.435 1.267 0.96
16 N3 N N3 N N N 0 7.145 -0.55 1.335
17 O1 O O1 N N N 0 -4.571 -1.0 -0.23
18 O2 O O2 N N N 0 -5.141 -2.968 1.417
19 O3 O O3 N N N 0 -6.606 -2.587 -0.733
20 O4 O O4 N N N 0 -4.226 -3.411 -0.893
21 O5 O O5 N N N 0 8.497 -0.225 -0.927
22 O6 O O6 N N N 0 7.473 -1.799 -2.092
23 O7 O O7 N N N 0 -0.549 3.494 0.226
24 P1 P P1 N N N 0 -5.117 -2.511 -0.126
25 S1 S S1 N N N 0 4.098 -0.467 1.064
26 H3 H H1 N N N 0 -2.379 5.206 -1.77
27 H2 H H2 N N N 0 -3.69 5.488 -0.6
28 H1 H H3 N N N 0 -1.998 5.46 -0.05
29 H12 H H4 N N N 0 5.565 0.705 -0.443
30 H13 H H5 N N N 0 4.891 -0.764 -1.19
31 H14 H H6 N N N 0 6.324 -2.165 0.271
32 H4 H H7 N N N 0 -5.047 1.158 -0.782
33 H5 H H8 N N N 0 -2.529 -1.174 -0.491
34 H6 H H9 N N N 0 -3.066 -0.865 1.178
35 H7 H H10 N N N 0 -0.795 -0.38 0.87
36 H17 H H18 N N N 0 7.387 0.421 1.207
37 H9 H H12 N N N 0 1.25 -0.537 1.651
38 H8 H H13 N N N 0 1.924 0.931 2.398
39 H11 H H14 N N N 0 2.34 0.055 -0.496
40 H10 H H15 N N N 0 3.014 1.523 0.251
41 H15 H H19 N N N 0 6.512 -0.666 2.113
42 H18 H H24 N N N 0 0.052 3.527 -0.531
43 H22 H H21 N N N 0 -5.707 -2.421 1.98
44 H23 H H22 N N N 0 -6.998 -3.471 -0.702
45 H24 H H23 N N N 0 8.144 -1.697 -2.78



X6I : Chemical Bonds

Total Number of Bonds: 45
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O5 C12 O C doub 1.21 N N
2 N3 C11 N C sing 1.47 N N
3 C12 C11 C C sing 1.51 N N
4 C12 O6 C O sing 1.34 N N
5 C11 C10 C C sing 1.53 N N
6 C10 S1 C S sing 1.81 N N
7 S1 C9 S C sing 1.81 N N
8 C9 C8 C C sing 1.53 N N
9 C8 N2 C N sing 1.46 N N
10 N2 C7 N C doub 1.29 N N
11 O7 C13 O C sing 1.36 N N
12 C7 C6 C C sing 1.48 N N
13 C13 C6 C C doub 1.4 N Y
14 C13 C2 C C sing 1.39 N Y
15 C1 C2 C C sing 1.51 N N
16 C6 C4 C C sing 1.4 N Y
17 C2 N1 C N doub 1.32 N Y
18 C4 C5 C C sing 1.51 N N
19 C4 C3 C C doub 1.38 N Y
20 C5 O1 C O sing 1.43 N N
21 N1 C3 N C sing 1.32 N Y
22 O1 P1 O P sing 1.61 N N
23 O4 P1 O P doub 1.48 N N
24 P1 O3 P O sing 1.61 N N
25 P1 O2 P O sing 1.61 N N
26 C1 H3 C H sing 1.09 N N
27 C1 H2 C H sing 1.09 N N
28 C1 H1 C H sing 1.09 N N
29 C10 H12 C H sing 1.09 N N
30 C10 H13 C H sing 1.09 N N
31 C11 H14 C H sing 1.09 N N
32 C3 H4 C H sing 1.08 N N
33 C5 H5 C H sing 1.09 N N
34 C5 H6 C H sing 1.09 N N
35 C7 H7 C H sing 1.08 N N
36 C8 H9 C H sing 1.09 N N
37 C8 H8 C H sing 1.09 N N
38 C9 H11 C H sing 1.09 N N
39 C9 H10 C H sing 1.09 N N
40 N3 H17 N H sing 1.01 N N
41 N3 H15 N H sing 1.01 N N
42 O2 H22 O H sing 0.97 N N
43 O3 H23 O H sing 0.97 N N
44 O6 H24 O H sing 0.97 N N
45 O7 H18 O H sing 0.97 N N



X6I : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
X6I 8t0v Open in New Window Bound ligand 1 1