Chemical Components in the PDB

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MTX : Summary

Code

MTX

One-letter code

X

Molecule name

METHOTREXATE

Systematic names

ProgramVersionName
ACDLabs 10.04 N-[(4-{[(2,4-diaminopteridin-6-yl)methyl](methyl)amino}phenyl)carbonyl]-L-glutamic acid
OpenEye OEToolkits 1.5.0 (2S)-2-[[4-[(2,4-diaminopteridin-6-yl)methyl-methyl-amino]phenyl]carbonylamino]pentanedioic acid

Formula

C20 H22 N8 O5

Formal charge

0

Molecular weight

454.439 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(NC(=O)c1ccc(cc1)N(C)Cc2nc3c(nc2)nc(nc3N)N)CCC(=O)O
SMILES CACTVS 3.341 CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)NC(CCC(=O)O)C(=O)O
Canonical SMILES CACTVS 3.341 CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)N[C@@H](CCC(=O)O)C(=O)O

IUPAC InChI

InChI=1S/C20H22N8O5/c1-28(9-11-8-23-17-15(24-11)16(21)26-20(22)27-17)12-4-2-10(3-5-12)18(31)25-13(19(32)33)6-7-14(29)30/h2-5,8,13H,6-7,9H2,1H3,(H,25,31)(H,29,30)(H,32,33)(H4,21,22,23,26,27)/t13-/m0/s1

IUPAC InChI key

FBOZXECLQNJBKD-ZDUSSCGKSA-N
MTX

wwPDB Information

Atom count

55 (33 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

2011-06-04

Status

Released

Obsoleted

Not Assigned



MTX : Atoms of Molecule

Total Number of Atoms: 55
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 2.395 0.559 5.47
2 C2 C C2 N Y N 0 2.31 0.209 6.738
3 NA2 N NA2 N N N 0 3.481 0.08 7.461
4 N3 N N3 N Y N 0 1.158 -0.024 7.359
5 C4 C C4 N Y N 0 0.0 0.081 6.723
6 NA4 N NA4 N N N 0 -1.192 -0.161 7.369
7 C4A C C4A N Y N 0 0.031 0.467 5.311
8 N5 N N5 N Y N 0 -1.077 0.604 4.591
9 C6 C C6 N Y N 0 -0.989 0.948 3.324
10 C7 C C7 N Y N 0 0.253 1.179 2.735
11 N8 N N8 N Y N 0 1.363 1.054 3.431
12 C8A C C8A N Y N 0 1.297 0.701 4.717
13 C9 C C9 N N N 0 -2.244 1.099 2.503
14 N10 N N10 N N N 0 -2.574 -0.182 1.875
15 CM C CM N N N 0 -3.438 -1.138 2.572
16 C11 C C11 N Y N 0 -1.056 -1.107 -1.887
17 C12 C C12 N Y N 0 -1.881 -2.019 -1.221
18 C13 C C13 N Y N 0 -2.381 -1.71 0.022
19 C14 C C14 N Y N 0 -2.067 -0.491 0.618
20 C15 C C15 N Y N 0 -1.25 0.42 -0.045
21 C16 C C16 N Y N 0 -0.742 0.114 -1.286
22 C C C N N N 0 -0.518 -1.436 -3.221
23 O O O N N N 0 -0.792 -2.5 -3.742
24 N N N N N N 0 0.276 -0.556 -3.862
25 CA C CA S N N 0 0.811 -0.882 -5.186
26 CT C CT N N N 0 2.135 -1.584 -5.034
27 O1 O O1 N N N 0 2.489 -2.392 -5.861
28 O2 O O2 N N N 0 2.922 -1.313 -3.981
29 CB C CB N N N 0 1.005 0.405 -5.989
30 CG C CG N N N 0 -0.339 1.118 -6.143
31 CD C CD N N N 0 -0.148 2.386 -6.933
32 OE1 O OE1 N N N 0 0.951 2.689 -7.333
33 OE2 O OE2 N N N 0 -1.198 3.18 -7.194
34 HN21 H 1HN2 N N N 0 3.448 -0.175 8.396
35 HN22 H 2HN2 N N N 0 4.335 0.246 7.033
36 HN41 H 1HN4 N N N 0 -1.193 -0.415 8.305
37 HN42 H 2HN4 N N N 0 -2.03 -0.078 6.887
38 H7 H H7 N N N 0 0.305 1.464 1.695
39 H91 H 1H9 N N N 0 -2.084 1.851 1.731
40 H92 H 2H9 N N N 0 -3.065 1.409 3.149
41 HM1 H 1HM N N N 0 -3.735 -0.724 3.535
42 HM2 H 2HM N N N 0 -4.326 -1.331 1.97
43 HM3 H 3HM N N N 0 -2.896 -2.071 2.729
44 H12 H H12 N N N 0 -2.125 -2.964 -1.682
45 H13 H H13 N N N 0 -3.018 -2.413 0.538
46 H15 H H15 N N N 0 -1.008 1.364 0.419
47 H16 H H16 N N N 0 -0.105 0.82 -1.798
48 HN H HN N N N 0 0.494 0.292 -3.446
49 HA H HA N N N 0 0.112 -1.535 -5.71
50 HO2 H HO2 N N N 0 3.772 -1.763 -3.884
51 HB1 H 1HB N N N 0 1.704 1.057 -5.465
52 HB2 H 2HB N N N 0 1.403 0.162 -6.974
53 HG1 H 1HG N N N 0 -1.038 0.465 -6.666
54 HG2 H 2HG N N N 0 -0.737 1.36 -5.157
55 HOE2 H 2HOE N N N 0 -1.075 3.994 -7.701



MTX : Chemical Bonds

Total Number of Bonds: 57
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C doub 1.32 N Y
2 N1 C8A N C sing 1.34 N Y
3 C2 NA2 C N sing 1.38 N N
4 C2 N3 C N sing 1.33 N Y
5 NA2 HN21 N H sing 0.97 N N
6 NA2 HN22 N H sing 0.97 N N
7 N3 C4 N C doub 1.33 N Y
8 C4 NA4 C N sing 1.38 N N
9 C4 C4A C C sing 1.46 N Y
10 NA4 HN41 N H sing 0.97 N N
11 NA4 HN42 N H sing 0.97 N N
12 C4A N5 C N sing 1.33 N Y
13 C4A C8A C C doub 1.42 N Y
14 N5 C6 N C doub 1.32 N Y
15 C6 C7 C C sing 1.39 N Y
16 C6 C9 C C sing 1.51 N N
17 C7 N8 C N doub 1.32 N Y
18 C7 H7 C H sing 1.08 N N
19 N8 C8A N C sing 1.34 N Y
20 C9 N10 C N sing 1.46 N N
21 C9 H91 C H sing 1.09 N N
22 C9 H92 C H sing 1.09 N N
23 N10 CM N C sing 1.47 N N
24 N10 C14 N C sing 1.39 N N
25 CM HM1 C H sing 1.09 N N
26 CM HM2 C H sing 1.09 N N
27 CM HM3 C H sing 1.09 N N
28 C11 C12 C C doub 1.4 N Y
29 C11 C16 C C sing 1.4 N Y
30 C11 C C C sing 1.48 N N
31 C12 C13 C C sing 1.37 N Y
32 C12 H12 C H sing 1.08 N N
33 C13 C14 C C doub 1.39 N Y
34 C13 H13 C H sing 1.08 N N
35 C14 C15 C C sing 1.39 N Y
36 C15 C16 C C doub 1.38 N Y
37 C15 H15 C H sing 1.08 N N
38 C16 H16 C H sing 1.08 N N
39 C O C O doub 1.22 N N
40 C N C N sing 1.35 N N
41 N CA N C sing 1.46 N N
42 N HN N H sing 0.97 N N
43 CA CT C C sing 1.51 N N
44 CA CB C C sing 1.53 N N
45 CA HA C H sing 1.09 N N
46 CT O1 C O doub 1.21 N N
47 CT O2 C O sing 1.34 N N
48 O2 HO2 O H sing 0.97 N N
49 CB CG C C sing 1.53 N N
50 CB HB1 C H sing 1.09 N N
51 CB HB2 C H sing 1.09 N N
52 CG CD C C sing 1.51 N N
53 CG HG1 C H sing 1.09 N N
54 CG HG2 C H sing 1.09 N N
55 CD OE1 C O doub 1.21 N N
56 CD OE2 C O sing 1.34 N N
57 OE2 HOE2 O H sing 0.97 N N



MTX : Used in PDB Entries

Total Number of PDB Entries: 56
Ligand Code PDB Entry ID Type Total Distinct
MTX 1ao8 Open in New Window Bound ligand 1 1
MTX 1axw Open in New Window Bound ligand 2 1
MTX 1d1g Open in New Window Bound ligand 2 1
MTX 1ddr Open in New Window Bound ligand 2 1
MTX 1dds Open in New Window Bound ligand 2 1
MTX 1df7 Open in New Window Bound ligand 1 1
MTX 1dhi Open in New Window Bound ligand 2 1
MTX 1dhj Open in New Window Bound ligand 2 1
MTX 1dls Open in New Window Bound ligand 1 1
MTX 1dra Open in New Window Bound ligand 2 1
MTX 1drb Open in New Window Bound ligand 2 1
MTX 1dre Open in New Window Bound ligand 1 1
MTX 1e7w Open in New Window Bound ligand 2 1
MTX 1mxf Open in New Window Bound ligand 4 1
MTX 1p33 Open in New Window Bound ligand 4 1
MTX 1ra3 Open in New Window Bound ligand 1 1
MTX 1rb3 Open in New Window Bound ligand 2 1
MTX 1rg7 Open in New Window Bound ligand 1 1
MTX 1rh3 Open in New Window Bound ligand 1 1
MTX 1rx3 Open in New Window Bound ligand 1 1
MTX 1tdr Open in New Window Bound ligand 2 1
MTX 1u70 Open in New Window Bound ligand 1 1
MTX 1u72 Open in New Window Bound ligand 1 1
MTX 2c7v Open in New Window Bound ligand 4 1
MTX 2drc Open in New Window Bound ligand 2 1
MTX 2oip Open in New Window Bound ligand 5 1
MTX 2qk8 Open in New Window Bound ligand 1 1
MTX 3cd2 Open in New Window Bound ligand 1 1
MTX 3cl9 Open in New Window Bound ligand 1 1
MTX 3dat Open in New Window Bound ligand 1 1
MTX 3dau Open in New Window Bound ligand 1 1
MTX 3dfr Open in New Window Bound ligand 1 1
MTX 3drc Open in New Window Bound ligand 2 1
MTX 3eig Open in New Window Bound ligand 1 1
MTX 3hj3 Open in New Window Bound ligand 4 1
MTX 3ia4 Open in New Window Bound ligand 4 1
MTX 3ix9 Open in New Window Bound ligand 2 1
MTX 3qxt Open in New Window Bound ligand 2 1
MTX 3qxv Open in New Window Bound ligand 5 1
MTX 3tq9 Open in New Window Bound ligand 1 1
MTX 4dfr Open in New Window Bound ligand 2 1
MTX 4gh8 Open in New Window Bound ligand 2 1
MTX 4kn0 Open in New Window Bound ligand 1 1
MTX 4ky8 Open in New Window Bound ligand 5 1
MTX 4l6h Open in New Window Bound ligand 1 1
MTX 4l8f Open in New Window Bound ligand 2 1
MTX 4l8w Open in New Window Bound ligand 2 1
MTX 4p66 Open in New Window Bound ligand 1 1
MTX 4p68 Open in New Window Bound ligand 1 1
MTX 4q0d Open in New Window Bound ligand 5 1
MTX 4qi9 Open in New Window Bound ligand 3 1
MTX 5hi6 Open in New Window Bound ligand 2 1
MTX 5j7w Open in New Window Bound ligand 2 1
MTX 5x66 Open in New Window Bound ligand 6 1
MTX 6deb Open in New Window Bound ligand 2 1
MTX 6ojs Open in New Window Bound ligand 5 1