Receptor
PDB id Resolution Class Description Source Keywords
1V0M 1.07 Å EC: 3.2.1.8 XYLANASE XYN10A FROM STREPTOMYCES LIVIDANS IN COMPLEX WITH X DEOXYNOJIRIMYCIN AT PH 7.5 STREPTOMYCES LIVIDANS GLYCOSIDE HYDROLASE FAMILY 10 XYLANASE XYLAN DEGRADATION DEOXYNOJIRIMYCIN HYDROLASE
Ref.: ATOMIC RESOLUTION ANALYSES OF THE BINDING OF XYLOBIOSE-DERIVED DEOXYNOJIRIMYCIN AND ISOFAGOMINE XYLANASE XYN10A CHEM.COMMUN.(CAMB.) V. 16 1794 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IMD A:1305;
 Invalid;
 none;
 submit data
69.085 C3 H5 N2 c1c[n...
XDN XYP A:1303;
 Valid;
 none;
 submit data
n/a n/a
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: XDN XYP; Similar ligands found: 0
No: Ligand ECFP6 Tc MDL keys Tc
Similar Ligands (3D)
Ligand no: 1; Ligand: XDN XYP; Similar ligands found: 493
No: Ligand Similarity coefficient
1 XDN XYP 1.0000
2 XYP XDN 0.9998
3 XDL XYP 0.9971
4 XYP XYP 0.9963
5 XIL 0.9897
6 XYS XYP 0.9728
7 XIF XYP 0.9705
8 XYP XIF 0.9686
9 XYS AZI XYS 0.9641
10 XYS XYS 0.9615
11 P2L 0.9526
12 XYP XYS 0.9366
13 ADN 0.9364
14 ZRK 0.9342
15 LOX XYP 0.9290
16 AFX 0.9262
17 TCC 0.9248
18 0SY 0.9235
19 C4E 0.9227
20 NOC 0.9224
21 5AD 0.9211
22 8OB 0.9209
23 3D8 0.9206
24 5FD 0.9205
25 4GU 0.9199
26 CC5 0.9196
27 833 0.9188
28 7EH 0.9183
29 WCU 0.9176
30 38E 0.9176
31 ISX 0.9158
32 ARJ 0.9157
33 5F1 0.9144
34 9JT 0.9144
35 6BK 0.9141
36 28A 0.9137
37 9CE 0.9124
38 AD3 0.9122
39 TCL 0.9122
40 5ID 0.9121
41 7L4 0.9119
42 AJ4 0.9110
43 NOS 0.9103
44 0OK 0.9101
45 AVX 0.9099
46 CBE 0.9096
47 27M 0.9095
48 272 0.9091
49 DXK 0.9090
50 DFL 0.9088
51 5E5 0.9087
52 F40 0.9084
53 FCW 0.9080
54 2QU 0.9080
55 C0H 0.9077
56 LR2 0.9076
57 NE1 0.9069
58 FHV 0.9066
59 3L1 0.9064
60 ZRL 0.9064
61 QME 0.9059
62 U13 0.9057
63 F18 0.9057
64 Y3J 0.9053
65 6WR 0.9050
66 20D 0.9050
67 BBY 0.9050
68 0UL 0.9046
69 A73 0.9044
70 1V1 0.9041
71 3CA 0.9040
72 6H2 0.9037
73 D9Z 0.9036
74 THU 0.9035
75 MJW 0.9034
76 B4L 0.9032
77 WLH 0.9022
78 P4L 0.9018
79 KWB 0.9015
80 4AU 0.9015
81 EAT 0.9011
82 4L2 0.9008
83 S0D 0.9008
84 MMA XYP 0.9003
85 6J3 0.9001
86 B5A 0.9001
87 XYP XIM 0.9001
88 GMP 0.8994
89 5I5 0.8992
90 LL1 0.8991
91 OLU 0.8988
92 EQW 0.8987
93 0X2 0.8986
94 L2K 0.8986
95 FB4 0.8986
96 LJ4 0.8984
97 1FL 0.8984
98 YE6 0.8982
99 TMG 0.8982
100 2JX 0.8980
101 3IP 0.8979
102 DCN 0.8975
103 848 0.8974
104 4Z1 0.8973
105 FHI 0.8972
106 51Y 0.8970
107 XYP AHR 0.8969
108 EXG 0.8969
109 5CD 0.8968
110 IMH 0.8968
111 3F4 0.8968
112 RGK 0.8965
113 92O 0.8963
114 8OE 0.8962
115 SZ5 0.8961
116 XCG 0.8958
117 3GX 0.8956
118 25F 0.8953
119 15Q 0.8953
120 X48 0.8952
121 TLF 0.8950
122 26C 0.8950
123 AOY 0.8949
124 397 0.8948
125 3AD 0.8946
126 Q4G 0.8946
127 3JC 0.8943
128 LVY 0.8942
129 2PV 0.8939
130 X2M 0.8939
131 6DQ 0.8938
132 LU2 0.8937
133 7VF 0.8937
134 L5D 0.8936
135 MZR 0.8935
136 EF2 0.8933
137 WVV 0.8932
138 2PK 0.8931
139 FZM 0.8929
140 TRP 0.8929
141 5CK 0.8926
142 KW7 0.8925
143 YUG 0.8925
144 II4 0.8923
145 5N5 0.8923
146 NKI 0.8922
147 2D2 0.8922
148 FPL 0.8922
149 68B 0.8921
150 4MP 0.8916
151 MJ5 0.8915
152 BGC BGC 0.8914
153 1SF 0.8913
154 AGI 0.8913
155 PRH 0.8912
156 2FA 0.8912
157 2GD 0.8911
158 6EL 0.8911
159 UKV 0.8910
160 5S9 0.8908
161 3D1 0.8908
162 4EU 0.8908
163 6QT 0.8906
164 AUV 0.8905
165 CUQ 0.8904
166 KF5 0.8904
167 HH6 0.8904
168 DSQ 0.8903
169 1XS 0.8903
170 DBE 0.8903
171 DBS 0.8902
172 4NR 0.8902
173 4FF 0.8900
174 4CN 0.8900
175 0FR 0.8900
176 A7Q 0.8899
177 JFS 0.8898
178 ID8 0.8896
179 V2Z 0.8894
180 50Q 0.8891
181 4G2 0.8889
182 NXB 0.8889
183 UA2 0.8886
184 TI7 0.8885
185 FMQ 0.8884
186 H75 0.8882
187 A51 0.8881
188 22L 0.8880
189 57D 0.8878
190 NAL 0.8877
191 CJZ 0.8877
192 MUK 0.8875
193 CH8 0.8874
194 IMK 0.8872
195 CUH 0.8870
196 IQW 0.8867
197 FT2 0.8867
198 XYA 0.8866
199 GZV 0.8864
200 M3W 0.8864
201 5VU 0.8863
202 1ZC 0.8863
203 J47 0.8863
204 D1Y 0.8860
205 TBN 0.8860
206 GNG 0.8859
207 1Q4 0.8858
208 A 0.8857
209 5C1 0.8857
210 EZN 0.8856
211 FY8 0.8856
212 S1D 0.8855
213 5NN 0.8853
214 N2Y 0.8851
215 JCZ 0.8851
216 2P3 0.8850
217 A4D 0.8849
218 EMU 0.8847
219 MTA 0.8847
220 ERZ 0.8846
221 JF8 0.8846
222 64I 0.8843
223 5CQ 0.8839
224 96Z 0.8839
225 IFM BGC 0.8838
226 DBM 0.8838
227 E9S 0.8837
228 Q0K 0.8837
229 08C 0.8836
230 NAR 0.8836
231 TGW 0.8835
232 KP2 0.8833
233 ENG 0.8832
234 SA0 0.8830
235 9FG 0.8829
236 BMC 0.8828
237 1AJ 0.8827
238 AJ6 0.8827
239 KYN 0.8827
240 120 0.8825
241 SOJ 0.8825
242 4ZF 0.8824
243 5WK 0.8822
244 M01 0.8821
245 AHR FUB 0.8821
246 7G1 0.8820
247 1DA 0.8818
248 OUA 0.8818
249 C2M 0.8818
250 XTS 0.8817
251 ZYV 0.8817
252 11X 0.8814
253 363 0.8814
254 EZB 0.8813
255 NEO 0.8812
256 AVA 0.8812
257 7G0 0.8812
258 IDZ 0.8812
259 FMB 0.8810
260 42R 0.8809
261 EV2 0.8809
262 16Z 0.8807
263 CJB 0.8807
264 FTU 0.8806
265 JSX 0.8806
266 DS8 0.8806
267 G14 0.8804
268 Z16 0.8803
269 FT3 0.8802
270 RPP 0.8802
271 L3L 0.8800
272 G30 0.8797
273 BNY 0.8797
274 3RP 0.8796
275 C53 0.8796
276 MTP 0.8795
277 GFE 0.8794
278 H7S 0.8793
279 CX5 0.8793
280 VT3 0.8792
281 MXD 0.8791
282 EKH 0.8791
283 S0G 0.8789
284 97K 0.8787
285 EDG AHR 0.8787
286 U14 0.8786
287 VIB 0.8786
288 DFV 0.8785
289 LI4 0.8784
290 Y70 0.8783
291 3WJ 0.8783
292 AKD 0.8783
293 DKX 0.8781
294 1YO 0.8781
295 A6H 0.8780
296 NU3 0.8777
297 7D7 0.8775
298 CTE 0.8773
299 DK4 0.8772
300 GPK 0.8770
301 9FH 0.8770
302 BGC OXZ 0.8768
303 1A5 0.8767
304 0OP 0.8765
305 2LT 0.8765
306 MHB 0.8762
307 A4V 0.8762
308 5E4 0.8760
309 3WK 0.8759
310 7ZO 0.8758
311 JA3 0.8756
312 VBC 0.8756
313 THM 0.8756
314 27F 0.8755
315 0ON 0.8754
316 ZZA 0.8753
317 XXX 0.8752
318 DAH 0.8752
319 NYJ 0.8750
320 BP3 0.8749
321 72E 0.8746
322 6DE 0.8745
323 8WB 0.8744
324 DKZ 0.8744
325 69K 0.8743
326 WDW 0.8742
327 PUR 0.8741
328 NIY 0.8741
329 3DE 0.8741
330 2GQ 0.8738
331 CL9 0.8738
332 FT1 0.8734
333 URI 0.8734
334 E3X 0.8732
335 14N 0.8730
336 DCZ 0.8729
337 4Z9 0.8728
338 B21 0.8727
339 1KN 0.8725
340 Q9T 0.8724
341 GLC IFM 0.8723
342 GJB 0.8720
343 MG7 0.8720
344 8D6 0.8720
345 1V8 0.8717
346 GLC BGC 0.8715
347 NW1 0.8713
348 BXZ 0.8712
349 GNW 0.8712
350 DZ1 0.8711
351 5OR 0.8710
352 3WO 0.8708
353 3WN 0.8708
354 CUT 0.8708
355 1ER 0.8707
356 EQA 0.8707
357 Z15 0.8706
358 43F 0.8705
359 9UL 0.8703
360 92G 0.8702
361 3Y7 0.8702
362 HO4 0.8702
363 TH1 0.8702
364 F4U 0.8701
365 AP6 0.8701
366 IDD 0.8701
367 BMZ 0.8701
368 X29 0.8700
369 DE7 0.8698
370 D64 0.8697
371 K80 0.8697
372 NIF 0.8696
373 TPM 0.8696
374 54F 0.8695
375 I0D 0.8694
376 Q2S 0.8694
377 BPY 0.8694
378 YIP 0.8691
379 MW5 0.8689
380 6MD 0.8688
381 NQ7 0.8687
382 CC6 0.8686
383 CDJ 0.8686
384 3VQ 0.8685
385 C4F 0.8684
386 H2W 0.8683
387 NPZ 0.8682
388 GXG 0.8681
389 HPR 0.8680
390 5M2 0.8680
391 CWE 0.8679
392 GJG 0.8679
393 6EN 0.8679
394 Z57 0.8676
395 4K2 0.8670
396 GLC 7LQ 0.8670
397 1V4 0.8668
398 W8L 0.8667
399 E9L 0.8666
400 OA4 0.8666
401 6J5 0.8666
402 HO6 0.8665
403 91F 0.8661
404 TJM 0.8661
405 O9Q 0.8660
406 GPQ 0.8658
407 FCD 0.8657
408 5JT 0.8657
409 M02 0.8657
410 LI7 0.8656
411 0NJ 0.8656
412 IEE 0.8655
413 GPU 0.8655
414 5DE 0.8655
415 DDC 0.8654
416 HX8 0.8653
417 MMS 0.8651
418 3Q0 0.8648
419 NEU 0.8647
420 GAL PHB 0.8646
421 2L1 0.8646
422 0OO 0.8643
423 JMG 0.8643
424 MQR 0.8640
425 JO5 0.8639
426 6MW 0.8638
427 5CJ 0.8636
428 OJD 0.8636
429 U4J 0.8636
430 ZEZ 0.8634
431 0GA 0.8633
432 OSP 0.8628
433 DMB 0.8623
434 56N 0.8623
435 ITW 0.8622
436 0XR 0.8620
437 A7K 0.8618
438 W29 0.8618
439 J84 0.8618
440 4F8 0.8616
441 5ER 0.8615
442 MIL 0.8614
443 KLE 0.8613
444 6NZ 0.8611
445 A4N 0.8611
446 A8K 0.8611
447 LZJ 0.8610
448 B2L 0.8610
449 FT6 0.8609
450 A18 0.8608
451 4YE 0.8607
452 531 0.8604
453 3VW 0.8602
454 MQS 0.8600
455 ESE 0.8597
456 O9Z 0.8596
457 YOF 0.8591
458 TC8 0.8591
459 A63 0.8587
460 ODK 0.8586
461 26A 0.8585
462 LZ5 0.8584
463 RVE 0.8582
464 IMV 0.8579
465 NK5 0.8578
466 TOH 0.8578
467 GAT 0.8578
468 U12 0.8576
469 3QI 0.8575
470 X6P 0.8573
471 FLF 0.8572
472 22F 0.8572
473 2L2 0.8570
474 TYP 0.8569
475 79W 0.8567
476 JPB 0.8564
477 5H6 0.8563
478 BVS 0.8560
479 GA2 0.8558
480 SJR 0.8558
481 CMG 0.8556
482 5UD 0.8553
483 U19 0.8552
484 A4T 0.8548
485 CFE 0.8548
486 DX2 0.8545
487 5R8 0.8543
488 V15 0.8536
489 4FP 0.8536
490 JPQ 0.8534
491 C93 0.8531
492 OA1 0.8521
493 Z2T 0.8515
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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