Receptor
PDB id Resolution Class Description Source Keywords
1OD8 1.05 Å EC: 3.2.1.8 XYLANASE XYN10A FROM STREPTOMYCES LIVIDANS IN COMPLEX WITH X ISOFAGOMINE LACTAM STREPTOMYCES LIVIDANS HYDROLASE/LECTIN GLYCOSIDE HYDROLASE FAMILY 10 XYLANASE XDEGRADATION TRANSITION STATE MIMIC ISOFAGOMINE LACTAM HYLECTIN HYDROLASE-LECTIN COMPLEX
Ref.: A XYLOBIOSE-DERIVED ISOFAGOMINE LACTAM GLYCOSIDASE BINDS AS ITS AMIDE TAUTOMER CHEM.COMMUN.(CAMB.) V. 8 944 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IMD A:1308;
A:1309;
 Invalid;
Invalid;
 none;
none;
 submit data
69.085 C3 H5 N2 c1c[n...
NA A:1303;
A:1304;
A:1305;
A:1312;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
22.99 Na [Na+]
XDL XYP A:1306;
A:1310;
 Valid;
Valid;
 none;
none;
 submit data
263.246 n/a O=C1C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1V0L 0.98 Å EC: 3.2.1.8 XYLANASE XYN10A FROM STREPTOMYCES LIVIDANS IN COMPLEX WITH X ISOFAGOMINE AT PH 5.8 STREPTOMYCES LIVIDANS GLYCOSIDE HYDROLASE FAMILY 10 XYLANASE XYLAN DEGRADATION ISOFAGOMINE HYDROLASE
Ref.: ATOMIC RESOLUTION ANALYSES OF THE BINDING OF XYLOBIOSE-DERIVED DEOXYNOJIRIMYCIN AND ISOFAGOMINE XYLANASE XYN10A CHEM.COMMUN.(CAMB.) V. 16 1794 2004
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 34 families.
1 1V0M - XDN XYP n/a n/a
2 1V0N - XIF XYP n/a n/a
3 1V0K Ki = 40 uM XYP XDN n/a n/a
4 1V0L Ki = 480 nM XIF XYP n/a n/a
5 1OD8 - XDL XYP n/a n/a
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 32 families.
1 1V0M - XDN XYP n/a n/a
2 1V0N - XIF XYP n/a n/a
3 1V0K Ki = 40 uM XYP XDN n/a n/a
4 1V0L Ki = 480 nM XIF XYP n/a n/a
5 1OD8 - XDL XYP n/a n/a
50% Homology Family (63)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 1V0M - XDN XYP n/a n/a
2 1V0N - XIF XYP n/a n/a
3 1V0K Ki = 40 uM XYP XDN n/a n/a
4 1V0L Ki = 480 nM XIF XYP n/a n/a
5 1OD8 - XDL XYP n/a n/a
6 3W25 - XYP XYP n/a n/a
7 3W27 - XYS XYP n/a n/a
8 3W26 - XYP XYP XYP n/a n/a
9 3W29 - XYS XYP XYP XYP n/a n/a
10 3W28 - XYS XYP XYP n/a n/a
11 1B30 - XYP XYP XYP n/a n/a
12 1B3V - XYS C5 H10 O5 C1[C@H]([C....
13 1B3Y - XYS C5 H10 O5 C1[C@H]([C....
14 1B3X - XYP XYP XYP n/a n/a
15 1B3Z - XYP XYP XYP n/a n/a
16 1ISY - BGC C6 H12 O6 C([C@@H]1[....
17 1V6W - XYP XYP n/a n/a
18 1ISX - XYP XYP n/a n/a
19 1ISZ - GAL C6 H12 O6 C([C@@H]1[....
20 1V6U - XYP XYP n/a n/a
21 1V6X - XYP XYP n/a n/a
22 1V6V - XYP XYP n/a n/a
23 2D24 - XYS XYS n/a n/a
24 2D23 - XYS AZI XYS n/a n/a
25 1IT0 - BGC GAL n/a n/a
26 1ISW - XYP XYP n/a n/a
27 2D20 - NPO C6 H5 N O3 c1cc(ccc1[....
28 1ISV - XYP C5 H10 O5 C1[C@H]([C....
29 3EMZ - HXH C19 H21 N O4 c1ccc(cc1)....
30 3WUE - XYP C5 H10 O5 C1[C@H]([C....
31 3WUG - XYP C5 H10 O5 C1[C@H]([C....
32 1FH7 Ki = 5.8 uM XYP XDN n/a n/a
33 1FHD Ki = 0.15 uM XYP XIM n/a n/a
34 1FH8 Ki = 0.13 uM XYP XIF n/a n/a
35 1J01 Ki = 0.34 uM XIL C10 H17 N O7 C1CNC(=O)[....
36 1FH9 Ki = 0.37 uM LOX XYP n/a n/a
37 5D4Y - XYP XYP n/a n/a
38 2FGL - XYS XYS n/a n/a
39 3NJ3 - XYP XYP n/a n/a
40 1VBR - XYP XYS n/a n/a
41 2BNJ - XYP XYP AHR FER n/a n/a
42 7K4X Kd = 13.04 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
43 5RGA - 6NT C6 H4 N4 O2 c1cc2c(cc1....
44 7K4Z - 6NT C6 H4 N4 O2 c1cc2c(cc1....
45 1GOR - XYS XYP n/a n/a
46 7K4Q Kd = 372.5 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
47 5RGD - 6NT C6 H4 N4 O2 c1cc2c(cc1....
48 7K4U - 6NT C6 H4 N4 O2 c1cc2c(cc1....
49 5RGC - 6NT C6 H4 N4 O2 c1cc2c(cc1....
50 4BS0 Ki = 2 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
51 3NYD - 3NY C6 H4 N4 O2 c1cc2c(cc1....
52 5RGB - 6NT C6 H4 N4 O2 c1cc2c(cc1....
53 5RGE - 6NT C6 H4 N4 O2 c1cc2c(cc1....
54 1GOQ - XYP XYP n/a n/a
55 5RGF - 6NT C6 H4 N4 O2 c1cc2c(cc1....
56 1UQY - XYP XYP XYP XYP n/a n/a
57 1UR1 - XYS XYP AHR n/a n/a
58 1UQZ - XYP XYP XYP GCV n/a n/a
59 3RDK - XYS XYP XYP GCV n/a n/a
60 5OFK - XYP XYP XYP XYP XYP XYP XYP n/a n/a
61 5OFL Ka = 17500 M^-1 BGC BGC BGC BGC BGC BGC n/a n/a
62 1R87 - XYP XYP n/a n/a
63 1HIZ - GLC C6 H12 O6 C([C@@H]1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: XDL XYP; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 XDL XYP 1 1
2 XIL 1 1
3 LOX XYP 0.492063 0.694915
4 XYP XYP XYP 0.426471 0.702128
5 XYP XIF 0.42623 0.788462
6 XYP XYP 0.423729 0.632653
7 XYP XDN 0.403226 0.764706
Similar Ligands (3D)
Ligand no: 1; Ligand: XDL XYP; Similar ligands found: 579
No: Ligand Similarity coefficient
1 XDN XYP 0.9971
2 XYS AZI XYS 0.9935
3 XYS XYP 0.9720
4 XIF XYP 0.9679
5 XYS XYS 0.9655
6 P2L 0.9437
7 XYP XYS 0.9403
8 ADN 0.9334
9 L2K 0.9307
10 ZRK 0.9298
11 CC5 0.9284
12 WCU 0.9276
13 AFX 0.9235
14 5AD 0.9232
15 0SY 0.9217
16 38E 0.9201
17 4GU 0.9199
18 6WR 0.9182
19 833 0.9182
20 NOC 0.9170
21 8OB 0.9167
22 9CE 0.9165
23 XYP AHR 0.9164
24 27M 0.9163
25 TCC 0.9159
26 C4E 0.9156
27 5F1 0.9147
28 9JT 0.9143
29 6BK 0.9142
30 5FD 0.9139
31 FCW 0.9125
32 ISX 0.9123
33 7EH 0.9122
34 TCL 0.9117
35 QME 0.9115
36 AVX 0.9114
37 ARJ 0.9113
38 F18 0.9111
39 U13 0.9111
40 CBE 0.9105
41 3L1 0.9102
42 28A 0.9098
43 AJ4 0.9092
44 AOY 0.9089
45 5S9 0.9087
46 1FL 0.9087
47 15Q 0.9085
48 AD3 0.9079
49 NOS 0.9079
50 WLH 0.9074
51 3F4 0.9074
52 26C 0.9073
53 XYP XIM 0.9072
54 F40 0.9072
55 RGK 0.9071
56 3D8 0.9070
57 2JX 0.9070
58 3IP 0.9069
59 MJW 0.9069
60 B4L 0.9067
61 PRH 0.9060
62 PQS 0.9053
63 2QV 0.9053
64 5CD 0.9052
65 0OK 0.9052
66 C0H 0.9052
67 SZ5 0.9051
68 DXK 0.9051
69 FHV 0.9044
70 3CA 0.9044
71 IQQ 0.9043
72 6P3 0.9041
73 7L4 0.9036
74 25F 0.9036
75 6H2 0.9035
76 Y3J 0.9035
77 2QU 0.9032
78 ZRL 0.9027
79 EAT 0.9026
80 0UL 0.9025
81 MMA XYP 0.9023
82 NXB 0.9022
83 FHI 0.9020
84 BBY 0.9020
85 H75 0.9020
86 OLU 0.9018
87 PCQ 0.9017
88 7VF 0.9017
89 LR2 0.9017
90 5I5 0.9016
91 3WO 0.9015
92 3WN 0.9015
93 0X2 0.9008
94 B5A 0.9007
95 7FZ 0.9007
96 848 0.9005
97 5CK 0.9005
98 IW1 0.9004
99 4AU 0.9004
100 P4L 0.9003
101 KW7 0.9002
102 5VU 0.8998
103 DFL 0.8997
104 272 0.8997
105 92O 0.8987
106 4EU 0.8986
107 TMG 0.8985
108 NE1 0.8984
109 FB4 0.8982
110 KF5 0.8975
111 613 0.8972
112 A73 0.8969
113 20D 0.8968
114 0NJ 0.8966
115 5B2 0.8964
116 1SF 0.8962
117 TRP 0.8962
118 TLF 0.8961
119 6EL 0.8956
120 1V1 0.8953
121 JFS 0.8953
122 UAY 0.8953
123 MUK 0.8952
124 YE6 0.8951
125 5E5 0.8950
126 L3L 0.8950
127 3D1 0.8949
128 4CN 0.8949
129 LJ4 0.8947
130 FY8 0.8946
131 THU 0.8945
132 CJZ 0.8945
133 NQ7 0.8943
134 DBE 0.8943
135 II4 0.8941
136 5WK 0.8941
137 4L2 0.8940
138 2FA 0.8939
139 8OE 0.8939
140 KWB 0.8938
141 OUA 0.8938
142 68B 0.8937
143 AUV 0.8936
144 7QY 0.8935
145 AGI 0.8935
146 ID8 0.8934
147 XCG 0.8934
148 S0D 0.8933
149 IDZ 0.8932
150 L5D 0.8932
151 X2M 0.8932
152 EQW 0.8931
153 4FF 0.8931
154 A51 0.8931
155 HH6 0.8930
156 51Y 0.8928
157 MZR 0.8928
158 3AD 0.8928
159 4MP 0.8926
160 NKI 0.8925
161 50Q 0.8924
162 WVV 0.8923
163 LU2 0.8923
164 TPM 0.8923
165 EES 0.8922
166 DBS 0.8922
167 EF2 0.8920
168 57D 0.8920
169 3JC 0.8919
170 JF8 0.8918
171 11X 0.8917
172 1ZC 0.8916
173 7W7 0.8916
174 IQW 0.8914
175 Q4G 0.8914
176 FZM 0.8913
177 FYR 0.8913
178 CUQ 0.8912
179 8WB 0.8911
180 H4B 0.8910
181 LVY 0.8910
182 M3W 0.8910
183 VT3 0.8910
184 C2M 0.8908
185 ERZ 0.8907
186 LI4 0.8905
187 5C1 0.8905
188 4Z1 0.8904
189 X48 0.8902
190 NW1 0.8901
191 Q11 0.8900
192 DCN 0.8899
193 A7Q 0.8898
194 EMU 0.8896
195 2PK 0.8895
196 FNA 0.8892
197 5N5 0.8892
198 LL1 0.8892
199 A 0.8891
200 JSX 0.8890
201 CTE 0.8889
202 ZSP 0.8889
203 1XS 0.8888
204 DSQ 0.8888
205 YUG 0.8888
206 PQM 0.8887
207 AHR FUB 0.8886
208 A4V 0.8884
209 6J3 0.8882
210 MHB 0.8882
211 GJB 0.8882
212 6DQ 0.8882
213 0DF 0.8881
214 TOH 0.8881
215 GAL FUC 0.8881
216 3GX 0.8880
217 4G2 0.8880
218 CUH 0.8880
219 1HP 0.8879
220 1V8 0.8878
221 3WK 0.8878
222 2P3 0.8878
223 TI7 0.8878
224 2GQ 0.8877
225 NAL 0.8876
226 2PV 0.8874
227 XYA 0.8873
228 14N 0.8871
229 96Z 0.8871
230 BP7 0.8871
231 S1D 0.8870
232 FMQ 0.8868
233 AJ6 0.8866
234 EQA 0.8865
235 22L 0.8862
236 6DE 0.8862
237 08C 0.8862
238 2GD 0.8861
239 HBI 0.8860
240 6WU 0.8859
241 N2Y 0.8859
242 XTS 0.8857
243 397 0.8857
244 WDW 0.8856
245 IFM BGC 0.8855
246 DE7 0.8855
247 DS8 0.8854
248 M01 0.8852
249 IMH 0.8852
250 EZN 0.8849
251 URI 0.8848
252 PLP 0.8848
253 A63 0.8847
254 5ID 0.8846
255 47V 0.8846
256 5CQ 0.8845
257 U14 0.8844
258 BGC BGC 0.8844
259 BGC OXZ 0.8844
260 1Q4 0.8843
261 TH1 0.8843
262 KP2 0.8842
263 97K 0.8842
264 D1Y 0.8841
265 A4D 0.8841
266 Y70 0.8841
267 2D2 0.8840
268 V2Z 0.8840
269 GXG 0.8839
270 5M2 0.8839
271 EZB 0.8837
272 MW5 0.8837
273 CWE 0.8836
274 IMK 0.8835
275 4NR 0.8834
276 3WJ 0.8834
277 A5Q 0.8833
278 ZZA 0.8832
279 NIY 0.8830
280 1V4 0.8830
281 BVS 0.8830
282 9MR 0.8826
283 C4F 0.8825
284 EDG AHR 0.8825
285 FPL 0.8825
286 KYN 0.8824
287 ENG 0.8824
288 GZV 0.8823
289 6J5 0.8822
290 1DA 0.8822
291 DFV 0.8821
292 FT2 0.8821
293 NU3 0.8820
294 6QT 0.8819
295 7G0 0.8818
296 TBN 0.8818
297 205 0.8818
298 G14 0.8817
299 1V3 0.8814
300 1AJ 0.8813
301 TGW 0.8813
302 42R 0.8813
303 16Z 0.8812
304 LR8 0.8809
305 64I 0.8809
306 AVA 0.8809
307 GPK 0.8806
308 MXD 0.8805
309 MJ5 0.8805
310 8D6 0.8805
311 E9S 0.8804
312 NAR 0.8803
313 AWE 0.8802
314 E9L 0.8801
315 UA2 0.8801
316 VBC 0.8798
317 AP6 0.8798
318 NYJ 0.8797
319 SA0 0.8795
320 LOT 0.8793
321 I0D 0.8793
322 363 0.8793
323 BXZ 0.8791
324 SOJ 0.8791
325 DAH 0.8791
326 5P3 0.8789
327 Q0K 0.8789
328 VJJ 0.8787
329 H7S 0.8787
330 4ZF 0.8786
331 ZYV 0.8785
332 C53 0.8784
333 9FH 0.8783
334 BNY 0.8782
335 1A5 0.8782
336 3RP 0.8780
337 69K 0.8780
338 ESE 0.8780
339 MTA 0.8779
340 3Y7 0.8779
341 Z16 0.8777
342 7G1 0.8777
343 0OO 0.8776
344 IEE 0.8775
345 5NN 0.8775
346 0ON 0.8774
347 MTP 0.8774
348 GXD 0.8773
349 H2W 0.8771
350 NE2 0.8769
351 FMC 0.8769
352 1KN 0.8768
353 CH8 0.8766
354 NEO 0.8764
355 72E 0.8763
356 5E4 0.8763
357 D9Z 0.8763
358 KMP 0.8763
359 0FR 0.8762
360 W8L 0.8761
361 GFE 0.8760
362 7ZO 0.8760
363 801 0.8759
364 22M 0.8759
365 OJD 0.8759
366 7D7 0.8759
367 120 0.8759
368 DK4 0.8757
369 DCZ 0.8757
370 RPP 0.8756
371 47X 0.8756
372 CJB 0.8756
373 3DE 0.8754
374 Q2S 0.8751
375 2M7 0.8751
376 CDJ 0.8750
377 BP3 0.8749
378 83D 0.8749
379 KLE 0.8748
380 JA3 0.8747
381 50C 0.8746
382 RE4 0.8746
383 IDD 0.8744
384 O9Q 0.8743
385 DDC 0.8741
386 TYP 0.8740
387 J47 0.8739
388 DZ1 0.8738
389 A9B 0.8737
390 HO4 0.8736
391 5NB 0.8736
392 6MD 0.8734
393 H2B 0.8734
394 CR4 0.8734
395 E3X 0.8733
396 9UL 0.8733
397 S0G 0.8733
398 JD7 0.8732
399 G30 0.8732
400 8UY 0.8732
401 5ER 0.8732
402 6EN 0.8732
403 0XR 0.8731
404 TJM 0.8731
405 A6H 0.8730
406 ZTW 0.8730
407 JZ8 0.8728
408 1ER 0.8728
409 FT3 0.8728
410 H35 0.8728
411 Z15 0.8727
412 Z57 0.8725
413 OA4 0.8725
414 CL9 0.8725
415 MMS 0.8723
416 VIB 0.8723
417 7ZL 0.8723
418 CTN 0.8722
419 0GA 0.8720
420 BMZ 0.8719
421 VC3 0.8716
422 JMG 0.8716
423 FT6 0.8715
424 GNW 0.8714
425 MG7 0.8710
426 4Z9 0.8710
427 NOY BGC 0.8709
428 SCE 0.8704
429 1UZ 0.8703
430 27F 0.8703
431 DKZ 0.8703
432 A7K 0.8703
433 FCD 0.8703
434 DKX 0.8698
435 NPZ 0.8698
436 A18 0.8693
437 GEN 0.8693
438 E6Q 0.8692
439 9FG 0.8692
440 GLC BGC 0.8692
441 BHS 0.8691
442 LJ3 0.8690
443 124 0.8689
444 GPQ 0.8689
445 3VQ 0.8685
446 5CJ 0.8685
447 6NZ 0.8684
448 KPV 0.8684
449 2L1 0.8683
450 LZJ 0.8683
451 JWS 0.8683
452 MIL 0.8681
453 3WL 0.8681
454 P4T 0.8680
455 F4U 0.8680
456 X29 0.8680
457 5AE 0.8680
458 6JO 0.8680
459 EV2 0.8679
460 DMB 0.8677
461 U4J 0.8677
462 M02 0.8676
463 IXM 0.8675
464 BPY 0.8675
465 72D 0.8674
466 BGC GAL 0.8674
467 789 0.8674
468 DGO Z61 0.8673
469 56N 0.8672
470 CUT 0.8672
471 43F 0.8671
472 GPU 0.8670
473 AHR AHR 0.8670
474 LI7 0.8669
475 AKD 0.8668
476 JGB 0.8668
477 GAL PHB 0.8668
478 K80 0.8667
479 D64 0.8667
480 GNG 0.8667
481 CMG 0.8667
482 PUR 0.8666
483 JNW 0.8666
484 4K2 0.8666
485 22F 0.8665
486 BIO 0.8663
487 RSV 0.8663
488 W29 0.8663
489 XXX 0.8662
490 531 0.8662
491 2L2 0.8661
492 7EL 0.8661
493 CMP 0.8661
494 5OR 0.8660
495 GCU BGC 0.8657
496 HPR 0.8657
497 MI2 0.8656
498 9RM 0.8656
499 B21 0.8655
500 Q9T 0.8655
501 4AB 0.8654
502 FTU 0.8652
503 0OP 0.8651
504 GMP 0.8651
505 GJG 0.8650
506 JPB 0.8647
507 FUB FUB 0.8647
508 54E 0.8646
509 X6W 0.8644
510 DTK 0.8641
511 697 0.8639
512 CU8 0.8639
513 SHG BGC 0.8639
514 KCH 0.8637
515 CC6 0.8637
516 MQR 0.8637
517 5P7 0.8634
518 EKH 0.8632
519 4FP 0.8632
520 MQS 0.8630
521 ZEZ 0.8629
522 EI1 0.8628
523 LZ5 0.8627
524 GA2 0.8625
525 HX8 0.8625
526 GAT 0.8621
527 7AP 0.8620
528 KLS 0.8620
529 CP6 0.8620
530 PA1 GCS 0.8615
531 3SU 0.8612
532 ELH 0.8609
533 NK5 0.8608
534 3Q0 0.8607
535 5DE 0.8607
536 FT1 0.8605
537 A8K 0.8604
538 RVE 0.8600
539 HHV 0.8598
540 AQ1 0.8598
541 7LU 0.8596
542 4YE 0.8594
543 3VW 0.8590
544 CX5 0.8588
545 BX4 0.8588
546 IFM BMA 0.8586
547 6MW 0.8586
548 7XX 0.8583
549 GCS GCS 0.8582
550 AX8 0.8578
551 J84 0.8578
552 JPQ 0.8577
553 GLC GAL 0.8574
554 A4T 0.8574
555 0NX 0.8573
556 L1T 0.8572
557 B2L 0.8570
558 5TO 0.8569
559 IXG 0.8567
560 FNT 0.8565
561 A4N 0.8564
562 LJ1 0.8564
563 C93 0.8563
564 Z70 0.8563
565 FC2 0.8559
566 MRI 0.8557
567 3QI 0.8556
568 A6Z 0.8555
569 ZEA 0.8554
570 5TU 0.8548
571 79W 0.8540
572 M2E 0.8538
573 U19 0.8537
574 1Q1 0.8536
575 YE7 0.8536
576 CFE 0.8535
577 Z2T 0.8519
578 3BH 0.8516
579 38B 0.8512
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1V0L; Ligand: XIF XYP; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 1v0l.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 4PMZ XYP XYP 40.5941
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