Chemical Components in the PDB

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IWA : Summary

Code

IWA

One-letter code

X

Molecule name

(2R)-2-azanyl-5-[[2-[3-methyl-2,6-bis(oxidanylidene)-7-(phenylmethyl)purin-8-yl]sulfanyl-3H-benzimidazol-5-yl]amino]-5-oxidanylidene-pentanoic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (2~{R})-2-azanyl-5-[[2-[3-methyl-2,6-bis(oxidanylidene)-7-(phenylmethyl)purin-8-yl]sulfanyl-3~{H}-benzimidazol-5-yl]amino]-5-oxidanylidene-pentanoic acid

Formula

C25 H24 N8 O5 S

Formal charge

0

Molecular weight

548.574 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN1C(=O)NC(=O)c2n(Cc3ccccc3)c(Sc4[nH]c5cc(NC(=O)CC[CH](N)C(O)=O)ccc5n4)nc12
SMILES OpenEye OEToolkits 2.0.7 CN1c2c(n(c(n2)Sc3[nH]c4cc(ccc4n3)NC(=O)CCC(C(=O)O)N)Cc5ccccc5)C(=O)NC1=O
Canonical SMILES CACTVS 3.385 CN1C(=O)NC(=O)c2n(Cc3ccccc3)c(Sc4[nH]c5cc(NC(=O)CC[C@@H](N)C(O)=O)ccc5n4)nc12
Canonical SMILES OpenEye OEToolkits 2.0.7 CN1c2c(n(c(n2)Sc3[nH]c4cc(ccc4n3)NC(=O)CC[C@H](C(=O)O)N)Cc5ccccc5)C(=O)NC1=O

IUPAC InChI

InChI=1S/C25H24N8O5S/c1-32-20-19(21(35)31-24(32)38)33(12-13-5-3-2-4-6-13)25(30-20)39-23-28-16-9-7-14(11-17(16)29-23)27-18(34)10-8-15(26)22(36)37/h2-7,9,11,15H,8,10,12,26H2,1H3,(H,27,34)(H,28,29)(H,36,37)(H,31,35,38)/t15-/m1/s1

IUPAC InChI key

XIOGIICTCSCBAE-OAHLLOKOSA-N
IWA

wwPDB Information

Atom count

63 (39 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-04-14

Last modified at

2022-09-02

Status

Released

Obsoleted

Not Assigned



IWA : Atoms of Molecule

Total Number of Atoms: 63
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N Y N 0 -4.073 -1.506 0.02
2 C5 C C2 N Y N 0 -5.068 -0.609 -0.353
3 C6 C C3 N N N 0 -6.416 -0.956 -0.154
4 C8 C C4 N Y N 0 -3.085 0.244 -0.8
5 N1 N N1 N N N 0 -6.716 -2.152 0.394
6 N3 N N2 N N N 0 -4.444 -2.717 0.582
7 N N N3 N N N 0 9.898 -0.274 -1.112
8 CA C C5 R N N 0 9.512 0.094 0.257
9 CAA C C6 N N N 0 -3.417 -3.682 0.985
10 CAH C C7 N Y N 0 -5.545 4.555 1.751
11 CAI C C8 N Y N 0 -6.551 3.649 1.472
12 CAJ C C9 N Y N 0 -4.38 4.546 1.008
13 CAK C C10 N Y N 0 -6.389 2.729 0.453
14 CAL C C11 N Y N 0 -4.22 3.629 -0.015
15 CAM C C12 N Y N 0 2.725 -2.662 0.325
16 CAN C C13 N Y N 0 1.372 -2.478 0.285
17 CAO C C14 N Y N 0 3.083 -0.493 -0.662
18 CAR C C15 N N N 0 -5.047 1.715 -1.401
19 C C C16 N N N 0 10.207 1.373 0.647
20 O O O1 N N N 0 10.643 2.109 -0.207
21 NAS N N4 N Y N 0 0.905 0.739 -1.15
22 NAV N N5 N Y N 0 -0.425 -0.832 -0.4
23 SAX S S1 N N N 0 -1.807 1.334 -1.332
24 CB C C17 N N N 0 7.997 0.295 0.323
25 CBA C C18 N Y N 0 -5.221 2.715 -0.286
26 CBB C C19 N Y N 0 3.588 -1.676 -0.145
27 CBC C C20 N Y N 0 -0.391 0.361 -0.938
28 CBG C C21 N Y N 0 1.711 -0.296 -0.709
29 CBH C C22 N Y N 0 0.843 -1.293 -0.232
30 CG C C23 N N N 0 7.294 -1.036 0.049
31 CD C C24 N N N 0 5.801 -0.838 0.115
32 NE2 N N6 N N N 0 4.973 -1.88 -0.096
33 OE1 O O2 N N N 0 5.345 0.26 0.357
34 OXT O O3 N N N 0 10.34 1.696 1.943
35 C2 C C25 N N N 0 -5.747 -3.012 0.751
36 O2 O O4 N N N 0 -6.054 -4.079 1.247
37 O6 O O5 N N N 0 -7.305 -0.185 -0.472
38 N7 N N7 N Y N 0 -4.418 0.501 -0.874
39 N9 N N8 N Y N 0 -2.898 -0.947 -0.27
40 H1 H H1 N N N 0 -7.645 -2.395 0.533
41 H2 H H2 N N N 0 9.638 0.448 -1.768
42 H3 H H3 N N N 0 10.885 -0.475 -1.168
43 H5 H H5 N N N 0 9.804 -0.701 0.942
44 H6 H H6 N N N 0 -3.13 -3.497 2.02
45 H7 H H7 N N N 0 -3.813 -4.693 0.893
46 H8 H H8 N N N 0 -2.545 -3.574 0.341
47 H9 H H9 N N N 0 -5.672 5.274 2.547
48 H10 H H10 N N N 0 -7.463 3.659 2.051
49 H11 H H11 N N N 0 -3.595 5.254 1.225
50 H12 H H12 N N N 0 -7.174 2.02 0.235
51 H13 H H13 N N N 0 -3.31 3.621 -0.595
52 H14 H H14 N N N 0 3.128 -3.578 0.73
53 H15 H H15 N N N 0 0.711 -3.249 0.652
54 H16 H H16 N N N 0 3.754 0.27 -1.027
55 H17 H H17 N N N 0 -6.021 1.467 -1.821
56 H18 H H18 N N N 0 -4.414 2.144 -2.178
57 H19 H H19 N N N 0 1.204 1.577 -1.536
58 H21 H H21 N N N 0 7.722 0.654 1.315
59 H22 H H22 N N N 0 7.695 1.027 -0.425
60 H23 H H23 N N N 0 7.569 -1.395 -0.943
61 H24 H H24 N N N 0 7.596 -1.768 0.798
62 H25 H H25 N N N 0 5.336 -2.772 -0.214
63 H26 H H26 N N N 0 10.793 2.527 2.144



IWA : Chemical Bonds

Total Number of Bonds: 67
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N CA N C sing 1.47 N N
2 O C O C doub 1.21 N N
3 CA C C C sing 1.51 N N
4 CA CB C C sing 1.53 N N
5 C OXT C O sing 1.34 N N
6 CAM CAN C C doub 1.37 N Y
7 CAM CBB C C sing 1.39 N Y
8 CG CB C C sing 1.53 N N
9 CG CD C C sing 1.51 N N
10 NE2 CBB N C sing 1.4 N N
11 NE2 CD N C sing 1.35 N N
12 CAN CBH C C sing 1.4 N Y
13 CBB CAO C C doub 1.39 N Y
14 CD OE1 C O doub 1.21 N N
15 O2 C2 O C doub 1.22 N N
16 CAJ CAH C C doub 1.38 N Y
17 CAJ CAL C C sing 1.38 N Y
18 CBH NAV C N sing 1.36 N Y
19 CBH CBG C C doub 1.41 N Y
20 CAA N3 C N sing 1.47 N N
21 C2 N3 C N sing 1.35 N N
22 C2 N1 C N sing 1.34 N N
23 CAH CAI C C sing 1.38 N Y
24 CAO CBG C C sing 1.39 N Y
25 N3 C4 N C sing 1.39 N N
26 N1 C6 N C sing 1.35 N N
27 NAV CBC N C doub 1.31 N Y
28 CAL CBA C C doub 1.38 N Y
29 CBG NAS C N sing 1.38 N Y
30 C4 C5 C C doub 1.39 N Y
31 C4 N9 C N sing 1.33 N Y
32 C6 C5 C C sing 1.41 N N
33 C6 O6 C O doub 1.22 N N
34 CAI CAK C C doub 1.38 N Y
35 C5 N7 C N sing 1.39 N Y
36 N9 C8 N C doub 1.32 N Y
37 CBC NAS C N sing 1.37 N Y
38 CBC SAX C S sing 1.76 N N
39 CBA CAK C C sing 1.38 N Y
40 CBA CAR C C sing 1.51 N N
41 N7 C8 N C sing 1.36 N Y
42 N7 CAR N C sing 1.47 N N
43 C8 SAX C S sing 1.76 N N
44 N1 H1 N H sing 0.97 N N
45 N H2 N H sing 1.01 N N
46 N H3 N H sing 1.01 N N
47 CA H5 C H sing 1.09 N N
48 CAA H6 C H sing 1.09 N N
49 CAA H7 C H sing 1.09 N N
50 CAA H8 C H sing 1.09 N N
51 CAH H9 C H sing 1.08 N N
52 CAI H10 C H sing 1.08 N N
53 CAJ H11 C H sing 1.08 N N
54 CAK H12 C H sing 1.08 N N
55 CAL H13 C H sing 1.08 N N
56 CAM H14 C H sing 1.08 N N
57 CAN H15 C H sing 1.08 N N
58 CAO H16 C H sing 1.08 N N
59 CAR H17 C H sing 1.09 N N
60 CAR H18 C H sing 1.09 N N
61 NAS H19 N H sing 0.97 N N
62 CB H21 C H sing 1.09 N N
63 CB H22 C H sing 1.09 N N
64 CG H23 C H sing 1.09 N N
65 CG H24 C H sing 1.09 N N
66 NE2 H25 N H sing 0.97 N N
67 OXT H26 O H sing 0.97 N N



IWA : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
IWA 7zif Open in New Window Bound ligand 1 1