Chemical Components in the PDB

pdbe.org/chem
spacer

F89 : Summary

Code

F89

One-letter code

X

Molecule name

S)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID

Synonyms

FOLATE ANALOG 1843U89

Systematic names

ProgramVersionName
ACDLabs 10.04 (2S)-2-(5-{[(3-methyl-1-oxo-1,2-dihydrobenzo[f]quinazolin-9-yl)methyl]amino}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)pentanedioic acid
OpenEye OEToolkits 1.5.0 (2S)-2-[6-[(3-methyl-1-oxo-2H-benzo[f]quinazolin-9-yl)methylamino]-3-oxo-1H-isoindol-2-yl]pentanedioic acid

Formula

C27 H24 N4 O6

Formal charge

0

Molecular weight

500.503 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(N5C(=O)c1c(cc(cc1)NCc4cc3c(ccc2N=C(NC(=O)c23)C)cc4)C5)CCC(=O)O
SMILES CACTVS 3.341 CC1=Nc2ccc3ccc(CNc4ccc5c(CN([CH](CCC(O)=O)C(O)=O)C5=O)c4)cc3c2C(=O)N1
SMILES OpenEye OEToolkits 1.5.0 CC1=Nc2ccc3ccc(cc3c2C(=O)N1)CNc4ccc5c(c4)CN(C5=O)C(CCC(=O)O)C(=O)O
Canonical SMILES CACTVS 3.341 CC1=Nc2ccc3ccc(CNc4ccc5c(CN([C@@H](CCC(O)=O)C(O)=O)C5=O)c4)cc3c2C(=O)N1
Canonical SMILES OpenEye OEToolkits 1.5.0 CC1=Nc2ccc3ccc(cc3c2C(=O)N1)CNc4ccc5c(c4)CN(C5=O)[C@@H](CCC(=O)O)C(=O)O

IUPAC InChI

InChI=1S/C27H24N4O6/c1-14-29-21-7-4-16-3-2-15(10-20(16)24(21)25(34)30-14)12-28-18-5-6-19-17(11-18)13-31(26(19)35)22(27(36)37)8-9-23(32)33/h2-7,10-11,22,28H,8-9,12-13H2,1H3,(H,32,33)(H,36,37)(H,29,30,34)/t22-/m0/s1

IUPAC InChI key

BRVFNEZMTRVUGW-QFIPXVFZSA-N
F89

wwPDB Information

Atom count

61 (37 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



F89 : Atoms of Molecule

Total Number of Atoms: 61
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 1.766 -0.399 5.729
2 O1A O O1A N N N 0 1.966 -0.832 4.608
3 N2 N N2 N Y N 0 2.774 -0.276 6.625
4 C3 C C3 N Y N 0 2.528 0.203 7.871
5 C3M C C3M N N N 0 3.681 0.314 8.835
6 N4 N N4 N Y N 0 1.35 0.576 8.272
7 C4A C C4A N Y N 0 0.27 0.506 7.466
8 C6A C C6A N Y N 0 -1.985 0.359 5.779
9 C5 C C5 N Y N 0 -1.001 0.913 7.908
10 C6 C C6 N Y N 0 -2.084 0.843 7.1
11 C7 C C7 N Y N 0 -3.111 0.288 4.945
12 C8 C C8 N Y N 0 -2.983 -0.184 3.673
13 C9 C C9 N Y N 0 -1.748 -0.599 3.186
14 C10 C C10 N Y N 0 -0.632 -0.543 3.969
15 N12 N N12 N N N 0 -1.354 -0.004 0.866
16 C1B C C1B N Y N 0 -0.728 -0.063 5.279
17 C1A C C1A N Y N 0 0.431 0.015 6.157
18 C11 C C11 N N N 0 -1.641 -1.117 1.775
19 C13 C C13 N Y N 0 -1.21 -0.238 -0.496
20 C14 C C14 N Y N 0 -0.943 0.82 -1.36
21 C15 C C15 N Y N 0 -0.797 0.586 -2.705
22 C16 C C16 N Y N 0 -0.926 -0.709 -3.216
23 C17 C C17 N Y N 0 -1.199 -1.768 -2.345
24 C18 C C18 N Y N 0 -1.34 -1.531 -0.997
25 C19 C C19 N N N 0 -0.508 1.482 -3.883
26 C C C N N N 0 -0.727 -0.651 -4.674
27 O O O N N N 0 -0.774 -1.611 -5.419
28 N N N N N N 0 -0.485 0.611 -5.064
29 CA C CA S N N 0 -0.24 1.047 -6.441
30 CT C CT N N N 0 -1.434 0.708 -7.295
31 O1 O O1 N N N 0 -1.709 1.396 -8.25
32 O2 O O2 N N N 0 -2.193 -0.357 -6.996
33 CB C CB N N N 0 0.997 0.333 -6.988
34 CG C CG N N N 0 2.209 0.677 -6.121
35 CD C CD N N N 0 3.428 -0.025 -6.661
36 OE1 O OE1 N N N 0 3.337 -0.728 -7.639
37 OE2 O OE2 N N N 0 4.616 0.13 -6.055
38 HN2 H HN2 N N N 0 3.674 -0.54 6.379
39 H3M1 H 1H3M N N N 0 3.324 0.717 9.783
40 H3M2 H 2H3M N N N 0 4.113 -0.672 9.0
41 H3M3 H 3H3M N N N 0 4.439 0.978 8.42
42 H5 H H5 N N N 0 -1.115 1.289 8.914
43 H6 H H6 N N N 0 -3.045 1.164 7.474
44 H7 H H7 N N N 0 -4.077 0.606 5.31
45 H112 H 2H11 N N N 0 -2.582 -1.587 1.488
46 H8 H H8 N N N 0 -3.852 -0.237 3.035
47 H10 H H10 N N N 0 0.32 -0.868 3.579
48 H111 H 1H11 N N N 0 -0.837 -1.85 1.717
49 HN12 H 2HN1 N N N 0 -1.264 0.895 1.216
50 H14 H H14 N N N 0 -0.842 1.823 -0.972
51 H17 H H17 N N N 0 -1.3 -2.772 -2.73
52 H18 H H18 N N N 0 -1.551 -2.35 -0.326
53 H191 H 1H19 N N N 0 -1.293 2.232 -3.986
54 H192 H 2H19 N N N 0 0.459 1.967 -3.757
55 HB2 H 2HB N N N 0 1.179 0.657 -8.013
56 HA H HA N N N 0 -0.075 2.124 -6.457
57 HO2 H HO2 N N N 0 -2.959 -0.575 -7.544
58 HB1 H 1HB N N N 0 0.832 -0.743 -6.972
59 HG1 H 1HG N N N 0 2.374 1.755 -6.138
60 HG2 H 2HG N N N 0 2.027 0.353 -5.097
61 HOE2 H 2HOE N N N 0 5.398 -0.32 -6.401



F89 : Chemical Bonds

Total Number of Bonds: 65
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 O1A C O doub 1.22 N N
2 C1 N2 C N sing 1.35 N Y
3 C1 C1A C C sing 1.46 N Y
4 N2 C3 N C sing 1.36 N Y
5 N2 HN2 N H sing 0.97 N N
6 C3 C3M C C sing 1.51 N N
7 C3 N4 C N doub 1.3 N Y
8 C3M H3M1 C H sing 1.09 N N
9 C3M H3M2 C H sing 1.09 N N
10 C3M H3M3 C H sing 1.09 N N
11 N4 C4A N C sing 1.35 N Y
12 C4A C5 C C doub 1.41 N Y
13 C4A C1A C C sing 1.41 N Y
14 C5 C6 C C sing 1.35 N Y
15 C5 H5 C H sing 1.08 N N
16 C6 C6A C C doub 1.41 N Y
17 C6 H6 C H sing 1.08 N N
18 C6A C7 C C sing 1.4 N Y
19 C6A C1B C C sing 1.42 N Y
20 C7 C8 C C doub 1.36 N Y
21 C7 H7 C H sing 1.08 N N
22 C8 C9 C C sing 1.39 N Y
23 C8 H8 C H sing 1.08 N N
24 C9 C10 C C doub 1.36 N Y
25 C9 C11 C C sing 1.51 N N
26 C10 C1B C C sing 1.4 N Y
27 C10 H10 C H sing 1.08 N N
28 C1B C1A C C doub 1.46 N Y
29 C11 N12 C N sing 1.47 N N
30 C11 H111 C H sing 1.09 N N
31 C11 H112 C H sing 1.09 N N
32 N12 C13 N C sing 1.39 N N
33 N12 HN12 N H sing 0.97 N N
34 C13 C14 C C doub 1.39 N Y
35 C13 C18 C C sing 1.39 N Y
36 C14 C15 C C sing 1.37 N Y
37 C14 H14 C H sing 1.08 N N
38 C15 C16 C C doub 1.4 N Y
39 C15 C19 C C sing 1.51 N N
40 C16 C17 C C sing 1.4 N Y
41 C16 C C C sing 1.47 N N
42 C17 C18 C C doub 1.38 N Y
43 C17 H17 C H sing 1.08 N N
44 C18 H18 C H sing 1.08 N N
45 C19 N C N sing 1.47 N N
46 C19 H191 C H sing 1.09 N N
47 C19 H192 C H sing 1.09 N N
48 C O C O doub 1.22 N N
49 C N C N sing 1.34 N N
50 N CA N C sing 1.47 N N
51 CA CT C C sing 1.51 N N
52 CA CB C C sing 1.53 N N
53 CA HA C H sing 1.09 N N
54 CT O1 C O doub 1.21 N N
55 CT O2 C O sing 1.34 N N
56 O2 HO2 O H sing 0.97 N N
57 CB CG C C sing 1.53 N N
58 CB HB1 C H sing 1.09 N N
59 CB HB2 C H sing 1.09 N N
60 CG CD C C sing 1.51 N N
61 CG HG1 C H sing 1.09 N N
62 CG HG2 C H sing 1.09 N N
63 CD OE1 C O doub 1.21 N N
64 CD OE2 C O sing 1.34 N N
65 OE2 HOE2 O H sing 0.97 N N



F89 : Used in PDB Entries

Total Number of PDB Entries: 6
Ligand Code PDB Entry ID Type Total Distinct
F89 1f28 Open in New Window Bound ligand 4 1
F89 1sej Open in New Window Bound ligand 10 1
F89 1syn Open in New Window Bound ligand 2 1
F89 1tlc Open in New Window Bound ligand 2 1
F89 1tsd Open in New Window Bound ligand 2 1
F89 2vf0 Open in New Window Bound ligand 2 1