Receptor
PDB id Resolution Class Description Source Keywords
2XD9 1.95 Å EC: 4.2.1.10 STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN C WITH INHIBITOR COMPOUND (4R,6R,7S)-4,6,7-TRIHYDROXY-2-((E)-E NYL)-4,5,6,7-TETRAHYDROBENZO(B) THIOPHENE-4-CARBOXYLIC ACI HELICOBACTER PYLORI AROMATIC AMINO ACID BIOSYNTHESIS LYASE
Ref.: TETRAHYDROBENZOTHIOPHENE DERIVATIVES: CONFORMATIONA RESTRICTED INHIBITORS OF TYPE II DEHYDROQUINASE. CHEMMEDCHEM V. 6 266 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
XD9 A:200;
B:200;
C:200;
Valid;
Valid;
Valid;
none;
none;
none;
Ki = 0.35 uM
270.302 C12 H14 O5 S CC=Cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2XD9 1.95 Å EC: 4.2.1.10 STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN C WITH INHIBITOR COMPOUND (4R,6R,7S)-4,6,7-TRIHYDROXY-2-((E)-E NYL)-4,5,6,7-TETRAHYDROBENZO(B) THIOPHENE-4-CARBOXYLIC ACI HELICOBACTER PYLORI AROMATIC AMINO ACID BIOSYNTHESIS LYASE
Ref.: TETRAHYDROBENZOTHIOPHENE DERIVATIVES: CONFORMATIONA RESTRICTED INHIBITORS OF TYPE II DEHYDROQUINASE. CHEMMEDCHEM V. 6 266 2011
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 2XDA Ki = 0.6 uM JPS C14 H18 O5 S c1c(sc2c1[....
2 2XD9 Ki = 0.35 uM XD9 C12 H14 O5 S CC=Cc1cc2c....
3 2C4W Ki = 20 uM GAJ C14 H9 N5 O4 S c1ccc2c(c1....
4 4B6R Ki = 1420 nM 9ZT C15 H18 O7 COc1ccc(cc....
5 4B6S Ki = 970 nM 2HN C14 H11 F5 O6 C1[C@H]([C....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2XDA Ki = 0.6 uM JPS C14 H18 O5 S c1c(sc2c1[....
2 2XD9 Ki = 0.35 uM XD9 C12 H14 O5 S CC=Cc1cc2c....
3 2C4W Ki = 20 uM GAJ C14 H9 N5 O4 S c1ccc2c(c1....
4 4B6R Ki = 1420 nM 9ZT C15 H18 O7 COc1ccc(cc....
5 4B6S Ki = 970 nM 2HN C14 H11 F5 O6 C1[C@H]([C....
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2XDA Ki = 0.6 uM JPS C14 H18 O5 S c1c(sc2c1[....
2 2XD9 Ki = 0.35 uM XD9 C12 H14 O5 S CC=Cc1cc2c....
3 2C4W Ki = 20 uM GAJ C14 H9 N5 O4 S c1ccc2c(c1....
4 4B6R Ki = 1420 nM 9ZT C15 H18 O7 COc1ccc(cc....
5 4B6S Ki = 970 nM 2HN C14 H11 F5 O6 C1[C@H]([C....
6 3N87 Ki = 11 uM N87 C20 H18 O6 c1ccc(cc1)....
7 2Y76 Ki = 440 nM CB7 C25 H22 O6 S2 c1cc2c(ccs....
8 3N7A Ki = 200 uM FA1 C7 H10 O5 C1[C@H]([C....
9 4B6O Ki = 100 nM 3DQ C15 H18 O7 COc1ccc(cc....
10 2Y71 Ki = 42.5 nM CB6 C17 H18 O6 S Cc1ccc2c(c....
11 4CIW Ki = 15 uM XH2 C9 H14 O6 C1[C@H]([C....
12 4B6P Ki = 74 nM 2HN C14 H11 F5 O6 C1[C@H]([C....
13 3N8N Ki = 27 uM N88 C12 H19 N O6 CC(C)(C)NC....
14 3N76 Ki = 0.14 uM CA2 C16 H22 O6 c1ccc(cc1)....
15 4CIY Ki = 27 uM NDY C15 H18 O6 c1ccc(cc1)....
16 1H0R Ki = 200 uM FA1 C7 H10 O5 C1[C@H]([C....
17 3N86 Ki = 2.3 uM RJP C16 H17 N O6 c1ccc(cc1)....
18 2XB8 Ki = 26 nM XNW C15 H18 O7 COc1ccc(cc....
19 1H0S - FA6 C7 H11 N O6 C1[C@H]([C....
20 4B6Q Ki = 28 nM BZ5 C16 H16 O6 S c1cc2c(ccs....
21 2Y77 Ki = 250 nM CB8 C21 H20 O6 S2 c1ccc2c(c1....
22 1GTZ - DHK C7 H10 O5 C1[C@@H](C....
23 2BT4 Ki = 33 uM CA2 C16 H22 O6 c1ccc(cc1)....
24 1V1J Ki = 15 uM FA3 C7 H9 F O5 C1[C@H]([C....
25 2CJF Ki = 380 nM RP4 C19 H18 O5 S c1ccc(cc1)....
26 1GU1 Ki = 30 uM FA1 C7 H10 O5 C1[C@H]([C....
27 3N8K Ki = 300 uM D1X C6 H5 N O4 C1C(=CC(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: XD9; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 XD9 1 1
2 JPS 0.471429 0.85
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2XD9; Ligand: XD9; Similar sites found: 242
This union binding pocket(no: 1) in the query (biounit: 2xd9.bio1) has 59 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1BTN I3P 0.02782 0.48935 None
2 3RF4 FUN 0.007896 0.47414 None
3 3KPE TM3 0.01843 0.46478 None
4 2JAR UMP 0.01334 0.43596 None
5 2PR5 FMN 0.03372 0.41827 None
6 3O55 FAD 0.02767 0.40723 None
7 3ZZS TRP 0.01157 0.40287 None
8 4OZJ ADP 0.02633 0.40181 None
9 5DRN 5CT 0.03354 0.47027 1.1976
10 3NGU ADP 0.01581 0.44256 1.3245
11 1Y1A GSH 0.03187 0.48492 1.79641
12 4QDC ASD 0.001419 0.45266 1.79641
13 4MOB ADP 0.02543 0.4281 1.79641
14 4L6C 0BT 0.01882 0.42109 1.79641
15 4PNI KQQ 0.01955 0.41546 1.79641
16 2W24 LYS 0.01392 0.41202 2
17 1PEA ACM 0.04128 0.45563 2.39521
18 3CEV ARG 0.01699 0.45262 2.39521
19 2ZO9 MLI 0.01483 0.44945 2.39521
20 2FOI JPA 0.01955 0.44554 2.39521
21 1MVQ MMA 0.001383 0.44333 2.39521
22 4GZP G39 0.000459 0.43935 2.39521
23 4HZO COA 0.03766 0.43901 2.39521
24 3IPQ 965 0.003844 0.43004 2.39521
25 4BPM LVJ 0.007031 0.42654 2.39521
26 4BPM GSH 0.009794 0.42478 2.39521
27 3TI8 LNV 0.003186 0.41327 2.39521
28 1S8F GDP 0.02594 0.40616 2.39521
29 3M31 FAD 0.04255 0.40415 2.39521
30 2A0S BIO 0.04807 0.40091 2.39521
31 5RHN 8BR 0.04304 0.41911 2.6087
32 1RYI GOA 0.01314 0.50765 2.87958
33 2NZ2 ASP 0.00004046 0.59167 2.99401
34 2NZ2 CIR 0.0001092 0.49634 2.99401
35 2Q8H TF4 0.0171 0.48471 2.99401
36 3ZPG 5GP 0.01916 0.48172 2.99401
37 2Z9V PXM 0.005982 0.48034 2.99401
38 4PB2 5UD 0.003819 0.45965 2.99401
39 1FNZ A2G 0.002508 0.457 2.99401
40 4IU0 ABH 0.004436 0.44687 2.99401
41 3MD0 GDP 0.03024 0.43996 2.99401
42 2PP3 LGT 0.0009991 0.43335 2.99401
43 4M37 SAH 0.01786 0.4275 2.99401
44 2BES RES 0.04009 0.42675 2.99401
45 1NU4 MLA 0.02486 0.45765 3.09278
46 2GNK ATP 0.0219 0.40179 3.57143
47 4LCQ URQ 0.00006783 0.49661 3.59281
48 2ZJ5 ADP 0.02026 0.45759 3.59281
49 2Z5Y HRM 0.0008336 0.4568 3.59281
50 2ZI8 SDT 0.0009755 0.4543 3.59281
51 3NKT 1HN 0.001974 0.44872 3.59281
52 4FUA PGH 0.002996 0.44185 3.59281
53 2C9O ADP 0.001432 0.4402 3.59281
54 1ML4 PAL 0.005496 0.43865 3.59281
55 1J2Z SOG 0.0003869 0.43046 3.59281
56 1I2L DCS 0.01921 0.42613 3.59281
57 1QZZ SAM 0.03676 0.42534 3.59281
58 3CH5 GDP 0.004218 0.42167 3.59281
59 1HV9 UD1 0.01075 0.40975 3.59281
60 1FWY UD1 0.01079 0.40971 3.59281
61 3EE4 MYR 0.04409 0.40811 3.59281
62 2FR6 URI 0.01441 0.4345 4.10959
63 1A5Z OXM 0.0001664 0.59453 4.19162
64 3EJ0 11X 0.002414 0.50349 4.19162
65 4HE2 AMP 0.00004533 0.49571 4.19162
66 2ZWS PLM 0.0211 0.49461 4.19162
67 1ONX ASP 0.0001788 0.48823 4.19162
68 1V6A TRE 0.00741 0.48076 4.19162
69 1I0Z OXM 0.04054 0.46197 4.19162
70 4P87 4NP 0.001551 0.45269 4.19162
71 4A8H PUW 0.0009079 0.45116 4.19162
72 1FX8 BOG 0.007392 0.45058 4.19162
73 2OWZ CIT 0.03924 0.44672 4.19162
74 1YBQ BDH 0.00058 0.44586 4.19162
75 2ZYF AKG 0.02987 0.44023 4.19162
76 2GN2 C5P 0.01405 0.43814 4.19162
77 2Q8M AMP 0.03541 0.42936 4.19162
78 1A5Z FBP 0.02002 0.42536 4.19162
79 2OWZ F6P 0.001424 0.42412 4.19162
80 1FW1 GSH 0.04067 0.42326 4.19162
81 2WLT ASP 0.008428 0.42003 4.19162
82 2Q6K ADN 0.007087 0.41293 4.19162
83 1RHC F42 ACN 0.0232 0.40186 4.19162
84 3NOJ PYR 0.003298 0.49643 4.20168
85 1CFV E3G 0.006277 0.43226 4.20168
86 4RLE 2BA 0.00911 0.41227 4.2735
87 1GXU 2HP 0.03009 0.41267 4.3956
88 4DN8 BMA 0.0008835 0.53657 4.48718
89 1OGD RIP 0.02512 0.44817 4.58015
90 1XX4 BAM 0.000309 0.54992 4.79042
91 1JN2 SFP 0.01081 0.51619 4.79042
92 3VOZ 04A 0.0003623 0.50877 4.79042
93 1A8S PPI 0.00144 0.49832 4.79042
94 2WL9 MBD 0.001007 0.46625 4.79042
95 2V5E SCR 0.04516 0.46556 4.79042
96 2F2U M77 0.01049 0.45881 4.79042
97 4GO7 THR 0.01182 0.45627 4.79042
98 1A59 CIT 0.03508 0.45437 4.79042
99 2P2V CSF 0.00004291 0.44591 4.79042
100 1UJ2 ADP 0.01273 0.42036 4.79042
101 1UJ2 C5P 0.01459 0.41806 4.79042
102 1A59 COA 0.04111 0.41446 4.79042
103 2ET1 GLV 0.003605 0.41354 4.79042
104 4KS1 2H8 0.004029 0.40293 4.79042
105 4ASJ N6A 0.04816 0.40195 4.79042
106 4G28 0W8 0.02269 0.44628 5.36913
107 1O7N IND 0.001233 0.46961 5.38922
108 4RJK PYR 0.02663 0.46682 5.38922
109 2QF7 COA 0.007937 0.45653 5.38922
110 2HFK E4H 0.03477 0.44082 5.38922
111 1FP2 SAH 0.02604 0.4324 5.38922
112 3IBH GSH 0.01752 0.42785 5.38922
113 3D2Y AH0 ALA FGA LYS 0.03876 0.4156 5.38922
114 3HAZ NAD 0.01054 0.41426 5.38922
115 3DER ALA LYS 0.03291 0.4135 5.38922
116 1WKL ADP 0.01404 0.43499 5.83942
117 1WKL ATP 0.01536 0.43328 5.83942
118 3VGL BGC 0.00001627 0.51927 5.98802
119 3I8P 840 0.01512 0.44 5.98802
120 1JQN DCO 0.001598 0.43607 5.98802
121 2JBH 5GP 0.03924 0.43421 5.98802
122 3VGL ANP 0.001674 0.42618 5.98802
123 4QDF 30Q 0.009246 0.42206 5.98802
124 3PC3 P1T 0.02254 0.42045 5.98802
125 1NHZ 486 0.02166 0.41858 5.98802
126 2GJN NIS 0.01268 0.41574 5.98802
127 1JCM 137 0.0121 0.41427 5.98802
128 1XP8 AGS 0.00186 0.41088 5.98802
129 1H8G CHT 0.022 0.49342 6.31579
130 1LSS NAD 0.04778 0.40662 6.42857
131 1RZM PEP 0.0068 0.47748 6.58683
132 1RZM E4P 0.04228 0.44974 6.58683
133 1ZJ6 G3D 0.01875 0.44266 6.58683
134 1AL8 FMN 0.0002247 0.42674 6.58683
135 3MAG SAH 0.01931 0.42604 6.58683
136 2FFC U5P 0.02319 0.42544 6.58683
137 3QP4 HL0 0.03381 0.42396 6.58683
138 1K27 MTM 0.004891 0.42167 6.58683
139 2Q28 ADP 0.0296 0.41805 6.58683
140 3TN7 NJP 0.0126 0.40938 6.58683
141 1E4I NFG 0.02737 0.40527 6.58683
142 2BJF DXC 0.006025 0.40118 6.58683
143 2HVK TBA 0.002791 0.50944 6.60377
144 3SQG COM 0.01556 0.4947 7.18563
145 1DXY COI 0.03909 0.46294 7.18563
146 1LYX PGA 0.0238 0.43424 7.18563
147 3L0E G58 0.01103 0.42036 7.18563
148 2Y7G AAE 0.0448 0.4183 7.18563
149 3K3G MMU 0.007936 0.47656 7.35294
150 4WK1 2BA 0.004802 0.42899 7.75194
151 3WSJ MK1 0.001238 0.41046 7.75862
152 1SS4 GSH 0.003878 0.54812 7.78443
153 1SS4 CIT 0.01072 0.50621 7.78443
154 3TKA CTN 0.03748 0.47884 7.78443
155 2BO4 FLC 0.02308 0.46469 7.78443
156 1F1V DHY 0.04394 0.43171 7.78443
157 3V91 UPG 0.0003886 0.42428 7.78443
158 1TFZ 869 0.02431 0.42174 7.78443
159 3OYZ ACO 0.003517 0.41688 7.78443
160 3TKA SAM 0.02744 0.41685 7.78443
161 1WNG SAH 0.04628 0.40964 7.78443
162 1F7K UMP 0.03525 0.40636 8.08823
163 4M7F BM3 0.00003182 0.59702 8.38323
164 1TV5 ORO 0.001269 0.48676 8.38323
165 1O9U ADZ 0.0467 0.45821 8.38323
166 4QN6 LNV 0.001062 0.4325 8.38323
167 1TV5 FMN 0.0007881 0.42774 8.38323
168 1W7J ADP BEF 0.02057 0.43073 8.60927
169 4M5P 23W 0.01765 0.47726 8.98204
170 3UXL CFI 0.00006064 0.46119 8.98204
171 4DYO SD4 0.0394 0.43412 8.98204
172 1EB9 HBA 0.034 0.43021 8.98204
173 4EA7 JB2 0.0002332 0.40577 8.98204
174 4EA7 COA 0.0002332 0.40577 8.98204
175 1VCO GLN 0.001264 0.45606 9.58084
176 1H16 PYR 0.04239 0.45495 9.58084
177 3P7I P7I 0.02479 0.44847 9.58084
178 4LKK SIA GAL 0.02556 0.42358 9.58084
179 1P1M MET 0.01803 0.42187 9.58084
180 1Q6O LG6 0.04056 0.4203 9.58084
181 1UGX GAL MGC 0.0008342 0.45679 9.77444
182 4Q3S X7A 0.003069 0.44008 10.1796
183 2VEZ G6P 0.01433 0.40944 10.5263
184 3TFC PEP 0.004577 0.48632 10.7784
185 4AF5 CIT 0.02013 0.46268 10.7784
186 1IZC PYR 0.001847 0.46243 10.7784
187 2GGH NLQ 0.000668 0.44383 10.7784
188 1F3L SAH 0.04762 0.40437 10.7784
189 2FH5 GTP 0.036 0.41438 11.3772
190 4EXO PYR 0.007019 0.50054 11.6438
191 3BY8 MLT 0.02633 0.46145 11.9718
192 4A8T PAO 0.000097 0.41703 11.976
193 1V8K ANP 0.0161 0.40559 11.976
194 3NYQ AMP 0.018 0.40007 11.976
195 4Q0A 4OA 0.009011 0.4434 12.5749
196 3I8T LBT 0.000836 0.52422 12.8049
197 1Y7P RIP 0.0241 0.45838 13.1737
198 3DG6 MUC 0.01305 0.44646 13.1737
199 1A27 EST 0.02919 0.4269 13.1737
200 3MMR ABH 0.03462 0.40342 13.1737
201 3CI3 5AD 0.008351 0.42018 13.7725
202 3CI3 3PO 0.008351 0.42018 13.7725
203 1K6M AGS 0.04337 0.40841 13.7725
204 2C5S AMP 0.009568 0.46515 14.3713
205 9LDT OXM 0.02511 0.48167 14.9701
206 2CE7 ADP 0.01936 0.43844 15.5689
207 2A2X NA9 0.01387 0.43522 15.5689
208 3L02 SN0 0.003212 0.42802 15.5689
209 3L02 CP 0.003212 0.42802 15.5689
210 3LEO GSH 0.009386 0.41831 15.5689
211 3HPF GAE 0.004095 0.41781 16.1677
212 4G4S LDZ 0.04272 0.41642 16.1677
213 1N9L FMN 0.02028 0.42799 16.5138
214 2J5S KTA 0.01353 0.43569 16.7665
215 5T63 ALA ALA ALA ALA 0.0492 0.40377 16.7665
216 4C2G ALA ALA ALA ALA 0.01946 0.44964 17.3653
217 1Y75 NAG 0.03473 0.43691 18.5629
218 1OYB HBA 0.01358 0.41691 19.1617
219 1OYB FMN 0.03504 0.4076 19.1617
220 1ECM TSA 0.02977 0.44031 19.2661
221 2BS5 BGC GAL FUC 0.01218 0.4211 20
222 2VAR AMP 0.04005 0.43015 20.3593
223 2VAR ANP 0.02335 0.4198 20.3593
224 3NJQ NJQ 0.0004159 0.47435 20.9581
225 1NXJ TLA 0.002138 0.47658 21.8579
226 1NXJ GLV 0.0122 0.45986 21.8579
227 4IEN COA 0.00518 0.4208 22.6994
228 4IEN GDP 0.01834 0.41082 22.6994
229 1JSH SIA GAL 0.03221 0.41144 23.2955
230 1G7V PAI 0.00113 0.42723 23.3533
231 2ORV 4TA 0.02993 0.40809 23.3533
232 2Q1A 2KT 0.005963 0.44161 23.9521
233 1G41 ADP 0.001208 0.40069 24.5509
234 2QLX RM4 0.005891 0.49808 25.9259
235 1N6B DMZ 0.00003332 0.48057 28.1437
236 2WR8 SAH 0.0003793 0.45195 28.1437
237 4AF0 MOA 0.0002409 0.49067 28.7425
238 4AF0 IMP 0.00007691 0.44359 28.7425
239 1KBI PYR 0.02675 0.40565 29.9401
240 1KBI FMN 0.02675 0.40565 29.9401
241 1BGV GLU 0.007826 0.40292 29.9401
242 2XBN PMP 0.002964 0.44486 42.515
Pocket No.: 2; Query (leader) PDB : 2XD9; Ligand: XD9; 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: 2xd9.bio1) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2XD9; Ligand: XD9; 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: 2xd9.bio1) has 59 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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