Receptor
PDB id Resolution Class Description Source Keywords
4KYS 2.18 Å EC: 2.5.1.2 CLOSTRIDIUM BOTULINUM THIAMINASE I IN COMPLEX WITH THIAMIN CLOSTRIDIUM BOTULINUM PERIPLASMIC BINDING PROTEIN TYPE 2 FOLD THIAMINASE I THIAMDEGRADATION TRANSFERASE
Ref.: STRUCTURE OF A CLOSTRIDIUM BOTULINUM C143S THIAMINA I/THIAMIN COMPLEX REVEALS ACTIVE SITE ARCHITECTURE. BIOCHEMISTRY V. 52 7830 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG B:504;
A:503;
A:504;
B:503;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
CIT A:502;
B:502;
Invalid;
Invalid;
none;
none;
submit data
192.124 C6 H8 O7 C(C(=...
VIB A:501;
B:501;
Valid;
Valid;
none;
none;
submit data
265.355 C12 H17 N4 O S Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4KYS 2.18 Å EC: 2.5.1.2 CLOSTRIDIUM BOTULINUM THIAMINASE I IN COMPLEX WITH THIAMIN CLOSTRIDIUM BOTULINUM PERIPLASMIC BINDING PROTEIN TYPE 2 FOLD THIAMINASE I THIAMDEGRADATION TRANSFERASE
Ref.: STRUCTURE OF A CLOSTRIDIUM BOTULINUM C143S THIAMINA I/THIAMIN COMPLEX REVEALS ACTIVE SITE ARCHITECTURE. BIOCHEMISTRY V. 52 7830 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4KYS - VIB C12 H17 N4 O S Cc1c(sc[n+....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4KYS - VIB C12 H17 N4 O S Cc1c(sc[n+....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4KYS - VIB C12 H17 N4 O S Cc1c(sc[n+....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: VIB; Similar ligands found: 10
No: Ligand ECFP6 Tc MDL keys Tc
1 VIB 1 1
2 TPS 0.686567 0.782609
3 TPP 0.621622 0.75
4 VNP 0.621622 0.72
5 TDP 0.605263 0.760563
6 TMV 0.605263 0.739726
7 V4E 0.589744 0.75
8 FTP 0.469136 0.73913
9 2TP 0.435294 0.697368
10 HMH 0.421053 0.603448
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4KYS; Ligand: VIB; Similar sites found: 70
This union binding pocket(no: 1) in the query (biounit: 4kys.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BOS GLA GAL 0.003456 0.40838 None
2 2BOS GLA GAL GLC 0.004355 0.40216 None
3 4FFG 0U8 0.003555 0.43077 1.63934
4 5GLT BGC GAL NAG GAL 0.0008753 0.40847 1.76056
5 2BMB PMM 0.01211 0.40848 1.87354
6 5EOB 5QQ 0.02149 0.43698 1.88088
7 5KBF CMP 0.01176 0.41134 1.99336
8 5F7V GLC GLC GLC GLC 0.01105 0.42223 2
9 4CLO XP0 0.009407 0.40793 2.08333
10 4LIT AKG 0.002991 0.42056 2.457
11 3TYZ PAB 0.007302 0.43791 2.5
12 2OFV 242 0.01209 0.43647 2.52708
13 4GCZ FMN 0.008679 0.42404 2.5974
14 2JIG PD2 0.01348 0.40134 2.67857
15 1A78 TDG 0.0006057 0.47324 2.98507
16 4Q0L V14 0.009287 0.43244 3.04183
17 5X7Q GLC GLC GLC GLC 0.003434 0.44182 3.27869
18 1N4W FAD 0.02107 0.43195 3.27869
19 2VEG PMM 0.005134 0.41203 3.50318
20 5JFS 6K0 0.00752 0.45192 3.57143
21 1SLT NDG GAL 0.00146 0.4515 3.73134
22 3FW9 SLX 0.01078 0.41925 3.74707
23 5H9P TD2 0.007033 0.41244 3.79747
24 5H9Q TD2 0.0002575 0.48539 3.87097
25 5T7I LAT NAG GAL 0.0008399 0.46092 3.87097
26 1WUB OTP 0.04372 0.41259 3.93258
27 4USF 6UI 0.01002 0.42769 3.94737
28 4YZC STU 0.03129 0.4151 3.95062
29 1A8U BEZ 0.01357 0.40074 3.97112
30 3ZY6 GFB 0.02608 0.40293 4.14365
31 4BCM T7Z 0.007775 0.41033 4.19847
32 2AGC DAO 0.004025 0.41575 4.32099
33 2ET1 GLV 0.004413 0.42565 4.47761
34 3ZXE PGZ 0.004513 0.40295 4.51128
35 4PSB GA3 0.03438 0.4108 4.51613
36 3NW7 LGV 0.04542 0.4133 4.56026
37 2YMZ LAT 0.0003489 0.46775 4.61538
38 1ULE GLA GAL NAG 0.0004194 0.47471 4.66667
39 2WEL K88 0.005679 0.40832 4.66667
40 1EOM NAG MAN MAN MAN NAG GAL NAG GAL 0.0136 0.41408 4.68384
41 1Y0G 8PP 0.02016 0.43129 4.71204
42 5FU3 BGC BGC BGC 0.009053 0.41088 4.71698
43 4K55 H6P 0.001038 0.40545 4.83871
44 2UVF AD0 0.0102 0.40981 4.93421
45 3WUC GLC GAL 0.01156 0.42287 5.10949
46 1O9U ADZ 0.000849 0.47085 5.14286
47 3K4Z XGP 0.004324 0.41635 5.19031
48 4XV1 904 0.0437 0.40405 5.47945
49 3WG3 A2G GAL NAG FUC 0.002541 0.42499 5.61798
50 4YLZ LAT NAG GAL 0.002005 0.4426 5.88235
51 5DYO FLU 0.0148 0.40206 5.9633
52 1ZM1 BGC BGC BGC 0.01824 0.40379 6.22407
53 5DG2 GAL GLC 0.0002261 0.4869 6.66667
54 4QDC ASD 0.008576 0.42034 6.92308
55 3M3E GAL A2G NPO 0.0001307 0.50538 7.45342
56 1W6P NDG GAL 0.002653 0.4482 8.20895
57 3OYW TDG 0.01095 0.40308 8.20895
58 4WVW SLT 0.0002034 0.49611 8.33333
59 5F3I 5UJ 0.01573 0.42314 8.33333
60 5KEW 6SB 0.0102 0.40763 8.51064
61 5HES 032 0.003369 0.44877 8.79479
62 3TTM PUT 0.0152 0.40062 9.82659
63 2ZHL NAG GAL GAL NAG 0.004203 0.40007 10.1351
64 3WV6 GAL BGC 0.001026 0.4415 10.473
65 3WV6 GAL GLC 0.002347 0.42185 10.473
66 1QKQ MAN 0.000836 0.44445 10.5634
67 5D3X 4IP 0.0177 0.40381 12.5749
68 1IS3 LAT 0.0008269 0.42194 12.5926
69 4U0I 0LI 0.01812 0.42239 13.0159
70 1C1L GAL BGC 0.002905 0.43368 13.1387
Pocket No.: 2; Query (leader) PDB : 4KYS; Ligand: VIB; Similar sites found: 14
This union binding pocket(no: 2) in the query (biounit: 4kys.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5H2D ERG 0.02879 0.40226 3.0445
2 5X7Q GLC GLC GLC GLC GLC 0.002357 0.44931 3.27869
3 3E7O 35F 0.02579 0.41418 3.33333
4 5T9C G3P 0.01221 0.4007 3.35821
5 2HFK E4H 0.005808 0.41648 3.51288
6 1M6P M6P 0.01185 0.40141 3.94737
7 1DMY AZM 0.008089 0.41479 4.03226
8 3NV3 GAL NAG MAN 0.0006432 0.40047 5.07246
9 2D6M LBT 0.0006424 0.40045 6.28931
10 5A3T MMK 0.04129 0.40316 7.06861
11 1GZW GAL BGC 0.009592 0.41467 8.20895
12 1W6O LAT 0.01035 0.41289 8.20895
13 2FB3 GTP 0.02892 0.41031 9.11765
14 1I82 BGC BGC 0.01408 0.40126 12.6984
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