Chemical Components in the PDB

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MIT : Summary

Code

MIT

One-letter code

X

Molecule name

amino{[(4S)-5-[(2R,4R)-2-carboxy-4-methylpiperidin-1-yl]-4-({[(3R)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}amino)-5-oxopentyl]amino}methaniminium

Synonyms

R-argatroban
MQPA
MD-805
MITSUBISHI INHIBITOR

Systematic names

ProgramVersionName
ACDLabs 12.01 amino{[(4S)-5-[(2R,4R)-2-carboxy-4-methylpiperidin-1-yl]-4-({[(3R)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}amino)-5-oxopentyl]amino}methaniminium
OpenEye OEToolkits 1.7.6 [azanyl-[[(4S)-5-[(2R,4R)-2-carboxy-4-methyl-piperidin-1-yl]-4-[[(3R)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonylamino]-5-oxidanylidene-pentyl]amino]methylidene]azanium

Formula

C23 H37 N6 O5 S

Formal charge

1

Molecular weight

509.642 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(N1C(C(=O)O)CC(C)CC1)C(NS(=O)(=O)c3cccc2c3NCC(C)C2)CCCNC(=[NH2+])\N
SMILES CACTVS 3.370 C[CH]1CCN([CH](C1)C(O)=O)C(=O)[CH](CCCNC(N)=[NH2+])N[S](=O)(=O)c2cccc3C[CH](C)CNc23
SMILES OpenEye OEToolkits 1.7.6 CC1CCN(C(C1)C(=O)O)C(=O)C(CCCNC(=[NH2+])N)NS(=O)(=O)c2cccc3c2NCC(C3)C
Canonical SMILES CACTVS 3.370 C[C@@H]1CCN([C@H](C1)C(O)=O)C(=O)[C@H](CCCNC(N)=[NH2+])N[S](=O)(=O)c2cccc3C[C@@H](C)CNc23
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@@H]1CCN([C@H](C1)C(=O)O)C(=O)[C@H](CCCNC(=[NH2+])N)NS(=O)(=O)c2cccc3c2NC[C@@H](C3)C

IUPAC InChI

InChI=1S/C23H36N6O5S/c1-14-8-10-29(18(12-14)22(31)32)21(30)17(6-4-9-26-23(24)25)28-35(33,34)19-7-3-5-16-11-15(2)13-27-20(16)19/h3,5,7,14-15,17-18,27-28H,4,6,8-13H2,1-2H3,(H,31,32)(H4,24,25,26)/p+1/t14-,15-,17+,18-/m1/s1

IUPAC InChI key

KXNPVXPOPUZYGB-XYVMCAHJSA-O

Has sub-components

34T , ARG , MCP
MIT

wwPDB Information

Atom count

72 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

peptide-like

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



MIT : Atoms of Molecule

Total Number of Atoms: 72
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C N N N 0 -0.827 1.303 -1.186
2 C1 C C1 N N N 0 -0.254 -1.544 2.608
3 C10 C C10 N N N 0 -2.01 -1.346 4.384
4 C11 C C11 R N N 0 -2.616 2.852 -0.558
5 C2 C C2 R N N 0 -1.762 -1.516 2.884
6 C21 C C21 N N N 0 -3.648 2.548 0.532
7 C3 C C3 N N N 0 -2.354 -2.845 2.409
8 C31 C C31 R N N 0 -3.044 2.858 1.903
9 C4 C C4 N Y N 0 -1.841 -3.163 1.027
10 C41 C C41 N N N 0 -1.82 1.969 2.136
11 C5 C C5 N Y N 0 -2.501 -4.136 0.293
12 C51 C C51 N N N 0 -0.769 2.263 1.066
13 C6 C C6 N Y N 0 -2.069 -4.47 -0.975
14 C61 C C61 N N N 0 -3.154 2.42 -1.898
15 C7 C C7 N Y N 0 -0.969 -3.831 -1.519
16 C71 C C71 N N N 0 -2.623 4.328 1.953
17 C8 C C8 N Y N 0 -0.31 -2.861 -0.796
18 C9 C C9 N Y N 0 -0.743 -2.517 0.485
19 CA C CA S N N 0 0.382 0.474 -0.834
20 CB C CB N N N 0 1.604 1.385 -0.701
21 CD C CD N N N 0 4.006 1.48 -0.022
22 CG C CG N N N 0 2.817 0.553 -0.282
23 CZ C CZ N N N 0 6.355 1.3 0.665
24 H H H N N N 0 0.504 -0.266 -2.82
25 H1 H H1 N N N 0 0.218 -0.673 3.062
26 H10 H H10 N N N 0 -1.564 -0.411 4.723
27 H10A H H10A N N N 0 -3.083 -1.326 4.575
28 H10B H H10B N N N 0 -1.561 -2.18 4.924
29 H11 H H11 N N N 0 -2.405 3.921 -0.574
30 H1A H H1A N N N 0 0.177 -2.454 3.026
31 H2 H H2 N N N 0 -2.221 -0.691 2.339
32 H21 H H21 N N N 0 -4.534 3.164 0.376
33 H22 H H22 N N N 0 -3.926 1.495 0.487
34 H3 H H3 N N N 0 -2.062 -3.638 3.096
35 H31 H H31 N N N 0 -3.785 2.666 2.679
36 H3A H H3A N N N 0 -3.441 -2.769 2.383
37 H41 H H41 N N N 0 -1.403 2.175 3.122
38 H42 H H42 N N N 0 -2.114 0.922 2.075
39 H5 H H5 N N N 0 -3.359 -4.636 0.716
40 H51 H H51 N N N 0 0.059 1.562 1.168
41 H52 H H52 N N N 0 -0.405 3.283 1.185
42 H6 H H6 N N N 0 -2.589 -5.229 -1.541
43 H7 H H7 N N N 0 -0.628 -4.092 -2.51
44 H71 H H71 N N N 0 -3.495 4.962 1.788
45 H72 H H72 N N N 0 -2.192 4.55 2.93
46 H73 H H73 N N N 0 -1.882 4.521 1.177
47 HA H HA N N N 0 0.207 -0.04 0.112
48 HB2 H HB2 N N N 0 1.805 1.865 -1.659
49 HB3 H HB3 N N N 0 1.408 2.148 0.053
50 HD2 H HD2 N N N 0 4.242 2.033 -0.931
51 HD3 H HD3 N N N 0 3.754 2.18 0.774
52 HE H HE N N N 0 5.096 -0.282 0.442
53 HG2 H HG2 N N N 0 2.582 0.0 0.627
54 HG3 H HG3 N N N 0 3.07 -0.147 -1.078
55 HH11 H HH11 N N N 0 5.685 3.153 0.314
56 HH12 H HH12 N N N 0 7.296 3.063 0.782
57 HH21 H HH21 N N N 0 8.253 1.013 1.233
58 HH22 H HH22 N N N 0 7.339 -0.389 1.093
59 HN H HN N N N 0 0.941 -1.553 0.936
60 HO21 H HO21 N N N 0 -3.847 3.017 -3.653
61 N N N N N N 0 -0.043 -1.518 1.159
62 N1 N N1 N N N 0 0.621 -0.513 -1.889
63 N2 N N2 N N N 0 -1.382 2.111 -0.261
64 NE N NE N N N 0 5.168 0.683 0.379
65 NH1 N NH1 N N N 0 6.454 2.626 0.579
66 NH2 N NH2 N N N 1 7.411 0.576 1.03
67 O O O N N N 0 -1.299 1.243 -2.301
68 O1 O O1 N N N 0 2.043 -1.923 -0.446
69 O11 O O11 N N N 0 -3.267 1.245 -2.154
70 O2 O O2 N N N 0 1.369 -2.714 -2.719
71 O21 O O21 N N N 0 -3.507 3.342 -2.808
72 S S S N N N 0 1.091 -2.051 -1.493



MIT : Chemical Bonds

Total Number of Bonds: 74
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 S C8 S C sing 1.76 N N
2 S O1 S O doub 1.42 N N
3 S N1 S N sing 1.66 N N
4 O2 S O S doub 1.42 N N
5 C1 C2 C C sing 1.53 N N
6 C1 H1 C H sing 1.09 N N
7 C1 H1A C H sing 1.09 N N
8 C2 C10 C C sing 1.53 N N
9 C2 H2 C H sing 1.09 N N
10 C3 C2 C C sing 1.53 N N
11 C3 H3 C H sing 1.09 N N
12 C3 H3A C H sing 1.09 N N
13 C4 C3 C C sing 1.51 N N
14 C5 C4 C C sing 1.39 N Y
15 C5 H5 C H sing 1.08 N N
16 C6 C5 C C doub 1.38 N Y
17 C6 H6 C H sing 1.08 N N
18 C7 C6 C C sing 1.38 N Y
19 C7 C8 C C doub 1.38 N Y
20 C7 H7 C H sing 1.08 N N
21 C8 C9 C C sing 1.4 N Y
22 C9 C4 C C doub 1.38 N Y
23 C9 N C N sing 1.39 N N
24 C10 H10 C H sing 1.09 N N
25 C10 H10A C H sing 1.09 N N
26 C10 H10B C H sing 1.09 N N
27 N C1 N C sing 1.46 N N
28 N1 CA N C sing 1.46 N N
29 N1 H N H sing 0.97 N N
30 CA C C C sing 1.51 N N
31 CA CB C C sing 1.53 N N
32 CA HA C H sing 1.09 N N
33 C O C O doub 1.21 N N
34 C N2 C N sing 1.35 N N
35 CB CG C C sing 1.53 N N
36 CB HB2 C H sing 1.09 N N
37 CB HB3 C H sing 1.09 N N
38 CG CD C C sing 1.53 N N
39 CG HG2 C H sing 1.09 N N
40 CG HG3 C H sing 1.09 N N
41 CD NE C N sing 1.47 N N
42 CD HD2 C H sing 1.09 N N
43 CD HD3 C H sing 1.09 N N
44 NE CZ N C sing 1.37 N N
45 NE HE N H sing 0.97 N N
46 CZ NH1 C N sing 1.33 N N
47 CZ NH2 C N doub 1.33 N N
48 NH1 HH11 N H sing 0.97 N N
49 NH1 HH12 N H sing 0.97 N N
50 NH2 HH21 N H sing 0.97 N N
51 NH2 HH22 N H sing 0.97 N N
52 N2 C11 N C sing 1.47 N N
53 N2 C51 N C sing 1.47 N N
54 C11 C21 C C sing 1.53 N N
55 C11 C61 C C sing 1.51 N N
56 C11 H11 C H sing 1.09 N N
57 C21 C31 C C sing 1.53 N N
58 C21 H21 C H sing 1.09 N N
59 C21 H22 C H sing 1.09 N N
60 C31 C41 C C sing 1.53 N N
61 C31 C71 C C sing 1.53 N N
62 C31 H31 C H sing 1.09 N N
63 C41 C51 C C sing 1.53 N N
64 C41 H41 C H sing 1.09 N N
65 C41 H42 C H sing 1.09 N N
66 C51 H51 C H sing 1.09 N N
67 C51 H52 C H sing 1.09 N N
68 C61 O11 C O doub 1.21 N N
69 C61 O21 C O sing 1.34 N N
70 O21 HO21 O H sing 0.97 N N
71 C71 H71 C H sing 1.09 N N
72 C71 H72 C H sing 1.09 N N
73 C71 H73 C H sing 1.09 N N
74 HN N H N sing 1.01 N N



MIT : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
MIT 1dwc Open in New Window Bound ligand 1 1
MIT 1etr Open in New Window Bound ligand 1 1