Chemical Components in the PDB

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L24 : Summary

Code

L24

One-letter code

X

Molecule name

[[[2-AMINO-5,6,7,8-TETRAHYDRO-4-HYDROXY-PYRIDO[2,3-D]PYRIMIDIN-6-YL]-ETHYL]-PHENYL]-CARBONYL-GLUTAMIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 N-[(4-{2-[(6S)-2-amino-4-hydroxy-5,6,7,8-tetrahydropyrido[2,3-d]pyrimidin-6-yl]ethyl}phenyl)carbonyl]-L-glutamic acid
OpenEye OEToolkits 1.5.0 (2S)-2-[[4-[2-[(6S)-2-amino-4-hydroxy-5,6,7,8-tetrahydropyrido[5,6-e]pyrimidin-6-yl]ethyl]phenyl]carbonylamino]pentanedioic acid

Formula

C21 H25 N5 O6

Formal charge

0

Molecular weight

443.453 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(NC(=O)c1ccc(cc1)CCC3Cc2c(nc(nc2NC3)N)O)CCC(=O)O
SMILES CACTVS 3.341 Nc1nc(O)c2C[CH](CCc3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O)CNc2n1
SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1CCC2Cc3c(nc(nc3O)N)NC2)C(=O)NC(CCC(=O)O)C(=O)O
Canonical SMILES CACTVS 3.341 Nc1nc(O)c2C[C@H](CCc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)CNc2n1
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1CC[C@H]2Cc3c(nc(nc3O)N)NC2)C(=O)N[C@@H](CCC(=O)O)C(=O)O

IUPAC InChI

InChI=1S/C21H25N5O6/c22-21-25-17-14(19(30)26-21)9-12(10-23-17)2-1-11-3-5-13(6-4-11)18(29)24-15(20(31)32)7-8-16(27)28/h3-6,12,15H,1-2,7-10H2,(H,24,29)(H,27,28)(H,31,32)(H4,22,23,25,26,30)/t12-,15-/m0/s1

IUPAC InChI key

ZUQBAQVRAURMCL-WFASDCNBSA-N
L24

wwPDB Information

Atom count

57 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-12-14

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



L24 : Atoms of Molecule

Total Number of Atoms: 57
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N2A N N2A N N N 0 -1.062 0.693 10.048
2 N1 N N1 N Y N 0 -1.447 0.281 7.781
3 C2 C C2 N Y N 0 -0.593 0.57 8.751
4 N3 N N3 N Y N 0 0.698 0.739 8.514
5 C4 C C4 N Y N 0 1.185 0.631 7.281
6 O4A O O4A N N N 0 2.508 0.807 7.047
7 C5 C C5 N Y N 0 0.317 0.334 6.236
8 C6 C C6 N Y N 0 -1.029 0.161 6.523
9 N7 N N7 N N N 0 -1.937 -0.14 5.52
10 C8 C C8 N N N 0 -1.528 0.022 4.118
11 C9 C C9 S N N 0 -0.125 -0.577 3.962
12 C10 C C10 N N N 0 0.85 0.213 4.835
13 C11 C C11 N N N 0 0.311 -0.492 2.498
14 C12 C C12 N N N 0 -0.665 -1.284 1.627
15 C1B C C1B N Y N 0 -0.234 -1.2 0.186
16 C2B C C2B N Y N 0 0.632 -2.147 -0.329
17 C3B C C3B N Y N 0 1.03 -2.076 -1.648
18 C4B C C4B N Y N 0 0.555 -1.046 -2.463
19 C5B C C5B N Y N 0 -0.318 -0.095 -1.936
20 C6B C C6B N Y N 0 -0.713 -0.18 -0.617
21 C7B C C7B N N N 0 0.978 -0.964 -3.877
22 O7B O O7B N N N 0 1.74 -1.794 -4.333
23 N N N N N N 0 0.518 0.03 -4.661
24 CA C CA S N N 0 0.937 0.112 -6.063
25 CB C CB N N N 0 -0.176 0.755 -6.891
26 CG C CG N N N 0 -1.445 -0.093 -6.787
27 CD C CD N N N 0 -2.542 0.539 -7.603
28 OE1 O OE1 N N N 0 -2.331 1.564 -8.206
29 OE2 O OE2 N N N 0 -3.754 -0.035 -7.659
30 C C C N N N 0 2.186 0.948 -6.166
31 O O O N N N 0 2.989 0.729 -7.043
32 OXT O OXT N N N 0 2.408 1.935 -5.284
33 HN21 H 1HN2 N N N 0 -2.006 0.575 10.235
34 HN22 H 2HN2 N N N 0 -0.447 0.9 10.768
35 HO4 H HO4 N N N 0 2.925 -0.061 7.135
36 HN7 H HN7 N N N 0 -2.829 -0.454 5.74
37 H81 H 1H8 N N N 0 -1.507 1.081 3.861
38 H82 H 2H8 N N N 0 -2.228 -0.501 3.466
39 H9 H H9 N N N 0 -0.137 -1.62 4.28
40 H101 H 1H10 N N N 0 0.985 1.209 4.413
41 H102 H 2H10 N N N 0 1.811 -0.3 4.858
42 H111 H 1H11 N N N 0 0.318 0.55 2.181
43 H112 H 2H11 N N N 0 1.312 -0.91 2.393
44 H121 H 1H12 N N N 0 -0.672 -2.327 1.944
45 H122 H 2H12 N N N 0 -1.666 -0.866 1.732
46 H2B H H2B N N N 0 0.998 -2.942 0.301
47 H3B H H3B N N N 0 1.707 -2.815 -2.05
48 H5B H H5B N N N 0 -0.689 0.703 -2.561
49 H6B H H6B N N N 0 -1.389 0.555 -0.208
50 HN H HN N N N 0 -0.089 0.692 -4.298
51 HA H HA N N N 0 1.138 -0.89 -6.441
52 HB1 H 1HB N N N 0 -0.378 1.757 -6.513
53 HB2 H 2HB N N N 0 0.134 0.815 -7.934
54 HG1 H 1HG N N N 0 -1.244 -1.096 -7.164
55 HG2 H 2HG N N N 0 -1.756 -0.154 -5.744
56 HE2 H HE2 N N N 0 -4.458 0.371 -8.183
57 HXT H HXT N N N 0 3.209 2.472 -5.35



L24 : Chemical Bonds

Total Number of Bonds: 59
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N2A C2 N C sing 1.38 N N
2 N2A HN21 N H sing 0.97 N N
3 N2A HN22 N H sing 0.97 N N
4 N1 C2 N C doub 1.32 N Y
5 N1 C6 N C sing 1.33 N Y
6 C2 N3 C N sing 1.32 N Y
7 N3 C4 N C doub 1.33 N Y
8 C4 O4A C O sing 1.36 N N
9 C4 C5 C C sing 1.39 N Y
10 O4A HO4 O H sing 0.97 N N
11 C5 C6 C C doub 1.39 N Y
12 C5 C10 C C sing 1.5 N N
13 C6 N7 C N sing 1.39 N N
14 N7 C8 N C sing 1.47 N N
15 N7 HN7 N H sing 0.97 N N
16 C8 C9 C C sing 1.53 N N
17 C8 H81 C H sing 1.09 N N
18 C8 H82 C H sing 1.09 N N
19 C9 C10 C C sing 1.53 N N
20 C9 C11 C C sing 1.53 N N
21 C9 H9 C H sing 1.09 N N
22 C10 H101 C H sing 1.09 N N
23 C10 H102 C H sing 1.09 N N
24 C11 C12 C C sing 1.53 N N
25 C11 H111 C H sing 1.09 N N
26 C11 H112 C H sing 1.09 N N
27 C12 C1B C C sing 1.51 N N
28 C12 H121 C H sing 1.09 N N
29 C12 H122 C H sing 1.09 N N
30 C1B C2B C C doub 1.38 N Y
31 C1B C6B C C sing 1.38 N Y
32 C2B C3B C C sing 1.38 N Y
33 C2B H2B C H sing 1.08 N N
34 C3B C4B C C doub 1.4 N Y
35 C3B H3B C H sing 1.08 N N
36 C4B C5B C C sing 1.39 N Y
37 C4B C7B C C sing 1.48 N N
38 C5B C6B C C doub 1.38 N Y
39 C5B H5B C H sing 1.08 N N
40 C6B H6B C H sing 1.08 N N
41 C7B O7B C O doub 1.22 N N
42 C7B N C N sing 1.35 N N
43 N CA N C sing 1.47 N N
44 N HN N H sing 0.97 N N
45 CA CB C C sing 1.53 N N
46 CA C C C sing 1.51 N N
47 CA HA C H sing 1.09 N N
48 CB CG C C sing 1.53 N N
49 CB HB1 C H sing 1.09 N N
50 CB HB2 C H sing 1.09 N N
51 CG CD C C sing 1.51 N N
52 CG HG1 C H sing 1.09 N N
53 CG HG2 C H sing 1.09 N N
54 CD OE1 C O doub 1.21 N N
55 CD OE2 C O sing 1.34 N N
56 OE2 HE2 O H sing 0.97 N N
57 C O C O doub 1.21 N N
58 C OXT C O sing 1.34 N N
59 OXT HXT O H sing 0.97 N N



L24 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
L24 1dia Open in New Window Bound ligand 1 1