Receptor
PDB id Resolution Class Description Source Keywords
1SBR 2.3 Å NON-ENZYME: BINDING THE STRUCTURE AND FUNCTION OF B. SUBTILIS YKOF GENE PRODUCT: THE COMPLEX WITH THIAMIN BACILLUS SUBTILIS YKOF THIAMIN-BINDING PROTEIN ACT-DOMAIN FAMILY X-RAY STRUCTURE LIGAND BINDING PROTEIN
Ref.: THE STRUCTURE AND LIGAND BINDING PROPERTIES OF THE B.SUBTILIS YKOF GENE PRODUCT, A MEMBER OF A NOVEL FAMILY OF THIAMIN/HMP-BINDING PROTEINS J.MOL.BIOL. V. 343 395 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:801;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
VIB A:501;
A:502;
B:503;
B:504;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 253 uM
265.355 C12 H17 N4 O S Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1SBR 2.3 Å NON-ENZYME: BINDING THE STRUCTURE AND FUNCTION OF B. SUBTILIS YKOF GENE PRODUCT: THE COMPLEX WITH THIAMIN BACILLUS SUBTILIS YKOF THIAMIN-BINDING PROTEIN ACT-DOMAIN FAMILY X-RAY STRUCTURE LIGAND BINDING PROTEIN
Ref.: THE STRUCTURE AND LIGAND BINDING PROPERTIES OF THE B.SUBTILIS YKOF GENE PRODUCT, A MEMBER OF A NOVEL FAMILY OF THIAMIN/HMP-BINDING PROTEINS J.MOL.BIOL. V. 343 395 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 473 families.
1 1SBR Kd = 253 uM 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 355 families.
1 1SBR Kd = 253 uM 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 272 families.
1 1SBR Kd = 253 uM 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 : 1SBR; Ligand: VIB; Similar sites found: 187
This union binding pocket(no: 1) in the query (biounit: 1sbr.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WT2 3UD 0.01051 0.43242 None
2 2QHD DAO 0.02803 0.42824 None
3 4RT1 C2E 0.007083 0.42453 None
4 5LGA 6VH 0.02835 0.41641 None
5 4M7V RAR 0.0422 0.41511 None
6 2QZT PLM 0.02242 0.41496 None
7 1GZF NIR 0.006297 0.41477 None
8 1YKI NFZ 0.03634 0.41052 None
9 1GZF ADP 0.01474 0.41043 None
10 1GZF NAD 0.01868 0.40878 None
11 3MBG FAD 0.02885 0.40652 None
12 5E7V M7E 0.03732 0.40436 None
13 3O55 FAD 0.03479 0.4022 None
14 1YMT DR9 0.02342 0.41396 1
15 1OJZ NAD 0.0149 0.4102 1
16 4RHP PEF 0.02158 0.40009 1
17 2X4Z X4Z 0.01721 0.42709 1.5
18 4M73 SAH 0.0444 0.40772 1.5
19 3H8C NSZ 0.03974 0.4052 1.5
20 3GKJ HC3 0.0223 0.40482 1.5
21 5JNN 6LM 0.02337 0.4085 1.57895
22 3BQD DAY 0.0007476 0.48233 2
23 4LSJ LSJ 0.00101 0.47563 2
24 3AQT RCO 0.0005575 0.47462 2
25 1NHZ 486 0.003033 0.45291 2
26 4P6X HCY 0.002618 0.45251 2
27 1DB1 VDX 0.02251 0.41967 2
28 5W4W 9WG 0.03227 0.40894 2
29 1UP7 NAD 0.02966 0.40588 2
30 3SVJ 4LI 0.02464 0.40422 2
31 5A7Y SAH 0.01435 0.4 2
32 4DSU BZI 0.002785 0.4116 2.1164
33 2A9K NAD 0.01689 0.41272 2.13904
34 5EWK P34 0.001219 0.43849 2.5
35 5A8E XTK 0.008548 0.43128 2.5
36 4J7Q B7N 0.01987 0.4248 2.5
37 2PNC CLU 0.00592 0.42278 2.5
38 3KYF 5GP 5GP 0.00245 0.41701 2.5
39 4MCC 21X 0.02019 0.4147 2.5
40 2Z9I GLY ALA THR VAL 0.01198 0.41273 2.5
41 3EFS BTN 0.0165 0.40979 2.5
42 2PT9 2MH 0.03895 0.40887 2.5
43 5F5N NAD 0.02803 0.40851 2.5
44 3WCA FPS 0.03446 0.40622 2.5
45 3LF0 ATP 0.003486 0.44979 2.63158
46 3KO0 TFP 0.006986 0.42301 2.9703
47 2AX9 BHM 0.009699 0.44689 3
48 1KUK PCA LYS TRP 0.003476 0.43542 3
49 3V49 PK0 0.009486 0.43047 3
50 1SOW NAD 0.01822 0.42463 3
51 2WN6 NDP 0.006614 0.42385 3
52 2XRH NIO 0.009233 0.41005 3
53 5CPR SAM 0.02635 0.40994 3
54 4MOB ADP 0.01224 0.40419 3
55 1GEG GLC 0.02084 0.40397 3
56 4K81 GTP 0.03585 0.40282 3
57 4XRZ SI6 0.03009 0.40126 3
58 4WZV E40 0.01217 0.42481 3.125
59 3QXV MTX 0.01068 0.41754 3.1746
60 4XSH NAI 0.0124 0.42287 3.35196
61 2BJ4 OHT 0.00106 0.47256 3.5
62 5AAV GW5 0.006094 0.4693 3.5
63 2QE4 JJ3 0.00583 0.46802 3.5
64 4TV1 36M 0.0007154 0.46057 3.5
65 4MGA 27L 0.001369 0.45522 3.5
66 4M8E 29V 0.004331 0.44493 3.5
67 1RX0 2MC 0.006041 0.44223 3.5
68 4POJ 2VP 0.005351 0.44185 3.5
69 3EF0 ALF 0.005161 0.43001 3.5
70 5XDT MB3 0.02662 0.41683 3.5
71 4MGB XDH 0.01141 0.41609 3.5
72 1Q0S SAH 0.0231 0.41022 3.5
73 3H0A 9RA 0.01629 0.41008 3.5
74 4MG7 27H 0.01641 0.40806 3.5
75 3UUD EST 0.01437 0.40696 3.5
76 1XL8 152 0.01077 0.4062 3.5
77 2OBD PCW 0.03767 0.40532 3.5
78 4KCF AKM 0.02855 0.40395 3.5
79 5DB3 58Q 0.02982 0.40146 3.5
80 5DXE EST 0.01857 0.40136 3.5
81 1HFS L04 0.01214 0.43411 3.75
82 3ESS 18N 0.01308 0.40008 3.91304
83 4MSG 2C6 0.004302 0.46067 4
84 5GS9 ARG 0.004287 0.43326 4
85 1OG1 TAD 0.01152 0.4213 4
86 4DQ2 BTX 0.02128 0.41743 4
87 1U6R IOM 0.01766 0.40144 4
88 5J8O 6GZ 0.01715 0.40514 4.03226
89 3PE2 E1B 0.01655 0.43779 4.1543
90 4NBI D3Y 0.01499 0.41702 4.26829
91 3TL1 JRO 0.004983 0.41971 4.40252
92 5CSD ACD 0.04496 0.40929 4.40252
93 5K3W PLP 0.008233 0.42124 4.5
94 2JIG PD2 0.01148 0.40478 4.5
95 1UOU CMU 0.01659 0.40383 4.5
96 3ZJ0 ACO 0.03126 0.4033 4.5
97 4RYV ZEA 0.00853 0.41366 4.51613
98 4USI ATP 0.01093 0.42247 4.54545
99 5L7G 6QE 0.001554 0.4679 5
100 4TWP AXI 0.01051 0.4478 5
101 5MW4 5JU 0.02556 0.42469 5
102 1WF3 GNP 0.02264 0.41208 5
103 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 0.01265 0.4027 5
104 5V3Y 5V8 0.01452 0.40223 5
105 4Z9D NAD 0.004998 0.43815 5.14286
106 2RCU BUJ 0.009775 0.457 5.5
107 5J75 6GQ 0.01008 0.41681 5.5
108 2Q2V NAD 0.04388 0.40501 5.5
109 1ZVX FIN 0.03538 0.41116 5.52147
110 1Q2C COA 0.02352 0.40685 5.55556
111 5U1M ACE LEU TYR ALA SER SER ASN PRO ALA PTR 0.005824 0.43286 5.71429
112 3IS2 FAD 0.02795 0.40986 5.84416
113 2VWA PTY 0.01587 0.40498 5.94059
114 1JR8 FAD 0.02417 0.40623 5.98291
115 4FK7 P34 0.0002253 0.49628 6
116 4OYA 1VE 0.01057 0.46069 6
117 3KMZ EQO 0.01621 0.42111 6
118 4FXQ G9L 0.003025 0.42091 6
119 3HY9 098 0.01418 0.41315 6
120 4RIF 3R2 0.03618 0.40261 6
121 1V3S ATP 0.003191 0.44811 6.03448
122 5A89 FMN 0.0425 0.41328 6.41026
123 5A89 ADP 0.0425 0.41328 6.41026
124 2E2R 2OH 0.002073 0.47772 6.5
125 5TIV A3P 0.02796 0.42341 6.5
126 3VRV YSD 0.04587 0.4154 6.5
127 1N62 MCN 0.03478 0.41357 6.5
128 5HGR 45D 0.03662 0.41034 6.5
129 4XDA ADP 0.03828 0.40929 6.5
130 5NTW 98N 0.04947 0.40002 6.5
131 2J9D AMP 0.003587 0.44154 6.72269
132 2J9C ATP 0.006536 0.44044 6.72269
133 2J9D ADP 0.006421 0.43438 6.72269
134 2Q1H AS4 0.00193 0.45725 7
135 4FMS BDP 0.001742 0.44185 7
136 5HGZ ACO 0.01812 0.41576 7
137 3B9Z CO2 0.02186 0.41103 7
138 5C5H 4YB 0.02423 0.41053 7
139 3TKY SAH 0.02495 0.4023 7
140 3QCQ 3Q0 0.03959 0.43665 7.37179
141 1SR7 MOF 0.002766 0.46718 7.5
142 2A3I C0R 0.002717 0.45357 7.5
143 2Q2Y ADP 0.0137 0.4377 7.5
144 2Q2Y MKR 0.01314 0.4377 7.5
145 4RVU NDP 0.02189 0.42251 7.5
146 2RH1 CAU 0.02052 0.40311 7.5
147 2TCL RO4 0.02702 0.40051 7.69231
148 3ZZH ARG 0.01129 0.40763 8
149 3U4C NDP 0.03332 0.40701 8
150 5K52 OCD 0.01679 0.41285 8.5
151 4RKK GLC GLC GLC GLC GLC GLC 0.01425 0.40714 8.5
152 4U0S ADP 0.01621 0.40433 8.5
153 4L2I NAD 0.03604 0.41976 9
154 4L2I FAD 0.02576 0.41971 9
155 5JO1 6LM 0.02624 0.40116 9
156 3G08 FEE 0.03372 0.4266 9.09091
157 1O44 852 0.005866 0.45675 9.25926
158 2YJD YJD 0.001427 0.45951 9.5
159 2I0G I0G 0.00962 0.45506 9.5
160 2BIF BOG 0.02771 0.40157 9.5
161 2ALG HP6 0.01469 0.41586 9.78261
162 2ALG DAO 0.01469 0.41585 9.78261
163 3KP6 SAL 0.01225 0.40905 9.93377
164 5IF4 6AK 0.01988 0.42686 10.0629
165 5XLY C2E 0.003084 0.44486 10.5
166 4GID 0GH 0.03635 0.44446 10.5
167 1O94 AMP 0.013 0.41509 10.5
168 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 0.003142 0.40889 10.5
169 2DYR PGV 0.03657 0.41237 10.9589
170 3Q2H QHF 0.0005549 0.40549 11
171 3RGA ILD 0.02401 0.40789 11.3074
172 2A5F NAD 0.00692 0.42287 11.4286
173 4PYW ACE THR THR ALA ILE NH2 0.01392 0.42025 11.5
174 3L0E G58 0.03906 0.40083 11.5
175 5DKK FMN 0.0261 0.40129 11.7241
176 3NC9 TR3 0.04417 0.40971 12
177 1VG0 GER 0.004779 0.42856 13
178 2LBD REA 0.02223 0.4111 13
179 2C49 ANP 0.01475 0.41575 13.5
180 4J4H 1J1 0.03936 0.41916 15
181 4J4H NAI 0.03936 0.41916 15
182 4JK3 NAD 0.0427 0.40121 15
183 3ACL 3F1 0.008047 0.42174 15.5
184 5X93 K87 0.01539 0.42364 17.5
185 2RDE C2E 0.002811 0.44 20
186 1FM9 9CR 0.004231 0.44185 44
187 3OLL EST 0.006811 0.42538 47.3684
Pocket No.: 2; Query (leader) PDB : 1SBR; Ligand: VIB; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1sbr.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1SBR; Ligand: VIB; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1sbr.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1SBR; Ligand: VIB; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1sbr.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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