Chemical Components in the PDB

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2E2 : Summary

Code

2E2

One-letter code

X

Molecule name

1-{3,5-O-[(4-carboxyphenyl)(phosphono)methylidene]-2-deoxy-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione

Systematic names

ProgramVersionName
ACDLabs 12.01 1-{3,5-O-[(4-carboxyphenyl)(phosphono)methylidene]-2-deoxy-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione
OpenEye OEToolkits 1.7.6 4-[(2R,4aR,6R,7aR)-6-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-phosphono-4a,6,7,7a-tetrahydro-4H-furo[3,2-d][1,3]dioxin-2-yl]benzoic acid

Formula

C18 H19 N2 O10 P

Formal charge

0

Molecular weight

454.325 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)c1ccc(cc1)C3(OCC4OC(N2C=C(C(=O)NC2=O)C)CC4O3)P(=O)(O)O
SMILES CACTVS 3.385 CC1=CN([CH]2C[CH]3O[C](OC[CH]3O2)(c4ccc(cc4)C(O)=O)[P](O)(O)=O)C(=O)NC1=O
SMILES OpenEye OEToolkits 1.7.6 CC1=CN(C(=O)NC1=O)C2CC3C(O2)COC(O3)(c4ccc(cc4)C(=O)O)P(=O)(O)O
Canonical SMILES CACTVS 3.385 CC1=CN([C@H]2C[C@H]3O[C@](OC[C@H]3O2)(c4ccc(cc4)C(O)=O)[P](O)(O)=O)C(=O)NC1=O
Canonical SMILES OpenEye OEToolkits 1.7.6 CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]3[C@H](O2)CO[C@@](O3)(c4ccc(cc4)C(=O)O)P(=O)(O)O

IUPAC InChI

InChI=1S/C18H19N2O10P/c1-9-7-20(17(24)19-15(9)21)14-6-12-13(29-14)8-28-18(30-12,31(25,26)27)11-4-2-10(3-5-11)16(22)23/h2-5,7,12-14H,6,8H2,1H3,(H,22,23)(H,19,21,24)(H2,25,26,27)/t12-,13-,14-,18-/m1/s1

IUPAC InChI key

FUFYAXRWQXEVGS-UHQDVWGKSA-N
2E2

wwPDB Information

Atom count

50 (31 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-09-26

Last modified at

2014-09-05

Status

Released

Obsoleted

Not Assigned



2E2 : Atoms of Molecule

Total Number of Atoms: 50
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O2 O O2 N N N 0 2.686 -0.579 2.45
2 C2 C C2 N N N 0 2.815 -0.792 1.26
3 N3 N N3 N N N 0 3.849 -0.244 0.596
4 C4 C C4 N N N 0 4.006 -0.47 -0.724
5 O4 O O4 N N N 0 4.942 0.025 -1.326
6 C5 C C5 N N N 0 3.072 -1.288 -1.405
7 CAR C CAR N N N 0 3.225 -1.557 -2.88
8 C6 C C6 N N N 0 2.044 -1.825 -0.714
9 N1 N N1 N N N 0 1.923 -1.575 0.626
10 CAJ C CAJ R N N 0 0.811 -2.163 1.376
11 OAF O OAF N N N 0 0.18 -3.183 0.592
12 CAI C CAI N N N 0 -0.252 -1.079 1.673
13 CAG C CAG R N N 0 -1.568 -1.859 1.457
14 OAH O OAH N N N 0 -2.637 -0.999 1.123
15 CAE C CAE R N N 0 -1.181 -2.799 0.296
16 CAC C CAC N N N 0 -1.152 -2.019 -1.022
17 OAD O OAD N N N 0 -2.34 -1.24 -1.162
18 CAB C CAB R N N 0 -2.503 -0.285 -0.106
19 PAA P PAA N N N 0 -4.0 0.712 -0.405
20 OBB O OBB N N N 0 -5.283 -0.257 -0.488
21 OBA O OBA N N N 0 -4.181 1.675 0.705
22 OBC O OBC N N N 0 -3.843 1.515 -1.791
23 CAU C CAU N Y N 0 -1.296 0.615 -0.043
24 CAV C CAV N Y N 0 -0.368 0.595 -1.069
25 CAW C CAW N Y N 0 0.74 1.416 -1.018
26 CAX C CAX N Y N 0 0.923 2.268 0.073
27 CCA C CCA N N N 0 2.106 3.15 0.135
28 OCB O OCB N N N 0 2.28 3.971 1.189
29 OCA O OCA N N N 0 2.923 3.135 -0.764
30 CAY C CAY N Y N 0 -0.018 2.283 1.105
31 CAZ C CAZ N Y N 0 -1.123 1.461 1.038
32 H1 H H1 N N N 0 4.485 0.316 1.069
33 H2 H H2 N N N 0 4.109 -1.04 -3.254
34 H3 H H3 N N N 0 3.334 -2.628 -3.045
35 H4 H H4 N N N 0 2.342 -1.196 -3.408
36 H5 H H5 N N N 0 1.322 -2.452 -1.217
37 H6 H H6 N N N 0 1.178 -2.587 2.311
38 H7 H H7 N N N 0 -0.171 -0.726 2.702
39 H8 H H8 N N N 0 -0.17 -0.25 0.971
40 H9 H H9 N N N 0 -1.807 -2.443 2.346
41 H10 H H10 N N N 0 -1.84 -3.666 0.247
42 H11 H H11 N N N 0 -0.284 -1.359 -1.032
43 H12 H H12 N N N 0 -1.082 -2.719 -1.854
44 H13 H H13 N N N 0 -6.116 0.206 -0.645
45 H14 H H14 N N N 0 -3.721 0.946 -2.563
46 H15 H H15 N N N 0 -0.511 -0.064 -1.913
47 H16 H H16 N N N 0 1.464 1.4 -1.819
48 H17 H H17 N N N 0 3.069 4.53 1.185
49 H18 H H18 N N N 0 0.118 2.94 1.952
50 H19 H H19 N N N 0 -1.852 1.472 1.835



2E2 : Chemical Bonds

Total Number of Bonds: 53
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OCA CCA O C doub 1.21 N N
2 OCB CCA O C sing 1.35 N N
3 O4 C4 O C doub 1.22 N N
4 CCA CAX C C sing 1.48 N N
5 C4 N3 C N sing 1.35 N N
6 C4 C5 C C sing 1.42 N N
7 CAR C5 C C sing 1.51 N N
8 CAX CAW C C doub 1.4 N Y
9 CAX CAY C C sing 1.4 N Y
10 N3 C2 N C sing 1.35 N N
11 C5 C6 C C doub 1.35 N N
12 CAW CAV C C sing 1.38 N Y
13 CAY CAZ C C doub 1.38 N Y
14 C2 O2 C O doub 1.22 N N
15 C2 N1 C N sing 1.35 N N
16 C6 N1 C N sing 1.37 N N
17 CAV CAU C C doub 1.38 N Y
18 CAZ CAU C C sing 1.38 N Y
19 N1 CAJ N C sing 1.46 N N
20 CAU CAB C C sing 1.51 N N
21 CAJ CAI C C sing 1.55 N N
22 CAJ OAF C O sing 1.43 N N
23 OAH CAB O C sing 1.43 N N
24 OAH CAG O C sing 1.41 N N
25 CAB OAD C O sing 1.43 N N
26 CAB PAA C P sing 1.82 N N
27 OAD CAC O C sing 1.43 N N
28 CAI CAG C C sing 1.54 N N
29 OAF CAE O C sing 1.44 N N
30 OBA PAA O P doub 1.48 N N
31 CAG CAE C C sing 1.54 N N
32 CAC CAE C C sing 1.53 N N
33 PAA OBB P O sing 1.61 N N
34 PAA OBC P O sing 1.61 N N
35 N3 H1 N H sing 0.97 N N
36 CAR H2 C H sing 1.09 N N
37 CAR H3 C H sing 1.09 N N
38 CAR H4 C H sing 1.09 N N
39 C6 H5 C H sing 1.08 N N
40 CAJ H6 C H sing 1.09 N N
41 CAI H7 C H sing 1.09 N N
42 CAI H8 C H sing 1.09 N N
43 CAG H9 C H sing 1.09 N N
44 CAE H10 C H sing 1.09 N N
45 CAC H11 C H sing 1.09 N N
46 CAC H12 C H sing 1.09 N N
47 OBB H13 O H sing 0.97 N N
48 OBC H14 O H sing 0.97 N N
49 CAV H15 C H sing 1.08 N N
50 CAW H16 C H sing 1.08 N N
51 OCB H17 O H sing 0.97 N N
52 CAY H18 C H sing 1.08 N N
53 CAZ H19 C H sing 1.08 N N



2E2 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
2E2 4mwo Open in New Window Bound ligand 1 1