Chemical Components in the PDB

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Y37 : Summary

Code

Y37

One-letter code

X

Molecule name

(1R,4R)-4-fluoro-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-2-ene-1-carboxylic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R,4R)-4-fluoro-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-2-ene-1-carboxylic acid
OpenEye OEToolkits 2.0.7 (1~{R},4~{R})-4-fluoranyl-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclopent-2-ene-1-carboxylic acid

Formula

C14 H18 F N2 O7 P

Formal charge

0

Molecular weight

376.274 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C1C(C(=CC1C(O)=O)NCc2c(cnc(C)c2O)COP(O)(O)=O)F
SMILES CACTVS 3.385 Cc1ncc(CO[P](O)(O)=O)c(CNC2=C[CH](C[CH]2F)C(O)=O)c1O
SMILES OpenEye OEToolkits 2.0.7 Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=CC(CC2F)C(=O)O)O
Canonical SMILES CACTVS 3.385 Cc1ncc(CO[P](O)(O)=O)c(CNC2=C[C@@H](C[C@H]2F)C(O)=O)c1O
Canonical SMILES OpenEye OEToolkits 2.0.7 Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=C[C@@H](C[C@H]2F)C(=O)O)O

IUPAC InChI

InChI=1S/C14H18FN2O7P/c1-7-13(18)10(9(4-16-7)6-24-25(21,22)23)5-17-12-3-8(14(19)20)2-11(12)15/h3-4,8,11,17-18H,2,5-6H2,1H3,(H,19,20)(H2,21,22,23)/t8-,11-/m1/s1

IUPAC InChI key

YUSFTNIOKSVGAN-LDYMZIIASA-N
Y37

wwPDB Information

Atom count

43 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-02-01

Last modified at

2022-02-11

Status

Released

Obsoleted

Not Assigned



Y37 : Atoms of Molecule

Total Number of Atoms: 43
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C20 C C1 N N N 0 4.545 -1.002 -1.322
2 C21 C C2 R N N 0 4.263 -1.315 0.166
3 C19 C C3 N N N 0 3.007 -0.539 0.491
4 C18 C C4 R N N 0 3.134 -0.636 -1.835
5 C17 C C5 N N N 0 2.387 -0.167 -0.608
6 C01 C C6 N N N 0 0.563 0.965 0.618
7 C02 C C7 N Y N 0 -0.695 1.737 0.312
8 C03 C C8 N Y N 0 -1.912 1.086 0.176
9 C04 C C9 N N N 0 -1.997 -0.41 0.333
10 C05 C C10 N Y N 0 -3.045 1.826 -0.103
11 C07 C C11 N Y N 0 -1.845 3.793 -0.115
12 C08 C C12 N N N 0 -1.828 5.291 -0.283
13 C09 C C13 N Y N 0 -0.665 3.119 0.165
14 C33 C C14 N N N 0 5.407 -0.846 1.027
15 F22 F F1 N N N 0 2.509 -1.761 -2.385
16 N06 N N1 N Y N 0 -2.981 3.136 -0.242
17 N11 N N2 N N N 0 1.204 0.561 -0.636
18 O10 O O1 N N N 0 0.503 3.801 0.295
19 O13 O O2 N N N 0 -3.125 -3.212 -0.947
20 O14 O O3 N N N 0 -3.35 -0.831 0.147
21 O15 O O4 N N N 0 -5.412 -2.463 0.113
22 O16 O O5 N N N 0 -3.389 -2.931 1.548
23 O34 O O6 N N N 0 5.362 -1.022 2.357
24 O35 O O7 N N N 0 6.365 -0.311 0.521
25 P12 P P1 N N N 0 -3.81 -2.372 0.244
26 H1 H H1 N N N 0 5.228 -0.157 -1.421
27 H2 H H2 N N N 0 4.934 -1.879 -1.839
28 H3 H H3 N N N 0 4.098 -2.383 0.304
29 H4 H H4 N N N 0 2.665 -0.321 1.492
30 H5 H H5 N N N 0 3.193 0.164 -2.572
31 H6 H H6 N N N 0 1.245 1.595 1.188
32 H7 H H7 N N N 0 0.313 0.079 1.201
33 H8 H H8 N N N 0 -1.362 -0.89 -0.412
34 H9 H H9 N N N 0 -1.663 -0.691 1.331
35 H10 H H10 N N N 0 -3.995 1.325 -0.211
36 H11 H H11 N N N 0 -2.001 5.766 0.683
37 H12 H H12 N N N 0 -0.858 5.601 -0.672
38 H13 H H13 N N N 0 -2.611 5.588 -0.98
39 H14 H H14 N N N 0 0.802 0.801 -1.486
40 H15 H H15 N N N 0 0.993 3.903 -0.533
41 H16 H H16 N N N 0 -3.358 -2.9 -1.832
42 H17 H H17 N N N 0 -5.76 -3.363 0.162
43 H18 H H18 N N N 0 6.119 -0.705 2.868



Y37 : Chemical Bonds

Total Number of Bonds: 44
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 F22 C18 F C sing 1.4 N N
2 C20 C18 C C sing 1.55 N N
3 C20 C21 C C sing 1.55 N N
4 C18 C17 C C sing 1.51 N N
5 O35 C33 O C doub 1.21 N N
6 C21 C33 C C sing 1.51 N N
7 C21 C19 C C sing 1.51 N N
8 O16 P12 O P doub 1.48 N N
9 C33 O34 C O sing 1.34 N N
10 C17 N11 C N sing 1.39 N N
11 C17 C19 C C doub 1.32 N N
12 O13 P12 O P sing 1.61 N N
13 N11 C01 N C sing 1.47 N N
14 P12 O15 P O sing 1.61 N N
15 P12 O14 P O sing 1.61 N N
16 C01 C02 C C sing 1.51 N N
17 C04 O14 C O sing 1.43 N N
18 C04 C03 C C sing 1.51 N N
19 C02 C03 C C sing 1.39 N Y
20 C02 C09 C C doub 1.39 N Y
21 C03 C05 C C doub 1.38 N Y
22 O10 C09 O C sing 1.36 N N
23 C09 C07 C C sing 1.39 N Y
24 C05 N06 C N sing 1.32 N Y
25 C07 N06 C N doub 1.32 N Y
26 C07 C08 C C sing 1.51 N N
27 C20 H1 C H sing 1.09 N N
28 C20 H2 C H sing 1.09 N N
29 C21 H3 C H sing 1.09 N N
30 C19 H4 C H sing 1.08 N N
31 C18 H5 C H sing 1.09 N N
32 C01 H6 C H sing 1.09 N N
33 C01 H7 C H sing 1.09 N N
34 C04 H8 C H sing 1.09 N N
35 C04 H9 C H sing 1.09 N N
36 C05 H10 C H sing 1.08 N N
37 C08 H11 C H sing 1.09 N N
38 C08 H12 C H sing 1.09 N N
39 C08 H13 C H sing 1.09 N N
40 N11 H14 N H sing 0.97 N N
41 O10 H15 O H sing 0.97 N N
42 O13 H16 O H sing 0.97 N N
43 O15 H17 O H sing 0.97 N N
44 O34 H18 O H sing 0.97 N N



Y37 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
Y37 7lk1 Open in New Window Bound ligand 3 1