Receptor
PDB id Resolution Class Description Source Keywords
1VBR 1.8 Å EC: 3.2.1.8 CRYSTAL STRUCTURE OF COMPLEX XYLANASE 10B FROM THERMOTOGA MA WITH XYLOBIOSE THERMOTOGA MARITIMA XYLANASE 10B HYDROLASE
Ref.: STRUCTURAL BASIS OF THE SUBSTRATE SUBSITE AND THE H THERMAL STABILITY OF XYLANASE 10B FROM THERMOTOGA M MSB8 PROTEINS V. 61 999 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACY A:3;
A:5;
A:6;
A:842;
B:2;
B:842;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
60.052 C2 H4 O2 CC(=O...
XYP XYS C:1;
D:1;
 Valid;
Valid;
 none;
none;
 submit data
n/a n/a
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1VBR 1.8 Å EC: 3.2.1.8 CRYSTAL STRUCTURE OF COMPLEX XYLANASE 10B FROM THERMOTOGA MA WITH XYLOBIOSE THERMOTOGA MARITIMA XYLANASE 10B HYDROLASE
Ref.: STRUCTURAL BASIS OF THE SUBSTRATE SUBSITE AND THE H THERMAL STABILITY OF XYLANASE 10B FROM THERMOTOGA M MSB8 PROTEINS V. 61 999 2005
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 34 families.
1 3NJ3 - XYP XYP n/a n/a
2 1VBR - XYP XYS n/a n/a
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 32 families.
1 3NJ3 - XYP XYP n/a n/a
2 1VBR - XYP XYS 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: XYP XYS; Similar ligands found: 0
No: Ligand ECFP6 Tc MDL keys Tc
Similar Ligands (3D)
Ligand no: 1; Ligand: XYP XYS; Similar ligands found: 331
No: Ligand Similarity coefficient
1 XYP XYS 1.0000
2 XYP XYP 0.9471
3 XYS XYS 0.9421
4 XDL XYP 0.9403
5 XYP XDN 0.9399
6 XYS XYP 0.9373
7 XDN XYP 0.9366
8 ADN 0.9312
9 LOX XYP 0.9305
10 XIF XYP 0.9294
11 XYS AZI XYS 0.9254
12 4GU 0.9250
13 WLH 0.9216
14 XIL 0.9214
15 XYP XIF 0.9202
16 WCU 0.9160
17 AFX 0.9130
18 ARJ 0.9126
19 5AD 0.9125
20 6H2 0.9107
21 IMH 0.9105
22 UA2 0.9085
23 LVY 0.9073
24 1DA 0.9072
25 NOC 0.9072
26 A 0.9071
27 5F1 0.9067
28 AD3 0.9066
29 5N5 0.9062
30 6WR 0.9062
31 TCL 0.9061
32 TBN 0.9057
33 NOS 0.9055
34 3IP 0.9036
35 YUG 0.9033
36 P2L 0.9026
37 FMC 0.9018
38 TCC 0.9011
39 GJB 0.9010
40 6SX 0.9010
41 5CD 0.9008
42 50Q 0.9007
43 FMB 0.9006
44 4L2 0.8999
45 GLC IFM 0.8995
46 F18 0.8977
47 FTU 0.8974
48 DCN 0.8971
49 3D8 0.8965
50 0X2 0.8964
51 NE1 0.8959
52 DSQ 0.8954
53 5CK 0.8952
54 PUR 0.8952
55 6J5 0.8951
56 FCW 0.8950
57 FY8 0.8950
58 3CA 0.8949
59 PRH 0.8946
60 HPR 0.8946
61 EF2 0.8946
62 NXB 0.8946
63 EKH 0.8943
64 TYP 0.8941
65 U13 0.8935
66 BNY 0.8933
67 CMP 0.8930
68 397 0.8929
69 FB4 0.8928
70 5FD 0.8920
71 5ID 0.8919
72 JAD 0.8918
73 38E 0.8912
74 GAL FUC 0.8906
75 15Q 0.8906
76 8OB 0.8902
77 833 0.8901
78 848 0.8899
79 Y3J 0.8895
80 7EH 0.8892
81 ZRK 0.8892
82 0OK 0.8889
83 CBE 0.8888
84 6WU 0.8888
85 20D 0.8881
86 XYP XIM 0.8880
87 C4F 0.8878
88 DFL 0.8876
89 5CJ 0.8876
90 0SY 0.8874
91 MYG 0.8872
92 6MD 0.8871
93 4K2 0.8869
94 QME 0.8868
95 3D1 0.8867
96 3L1 0.8862
97 GLC 7LQ 0.8860
98 ID8 0.8859
99 TLF 0.8858
100 3AD 0.8856
101 J27 0.8856
102 CC5 0.8856
103 1V1 0.8855
104 3WJ 0.8854
105 AX4 0.8854
106 C4E 0.8854
107 6EL 0.8854
108 D64 0.8852
109 MUK 0.8849
110 DGO Z61 0.8849
111 MMA XYP 0.8849
112 6SZ 0.8848
113 QRP 0.8847
114 XYA 0.8844
115 FT3 0.8839
116 2FA 0.8838
117 EMU 0.8838
118 5I5 0.8838
119 9JT 0.8837
120 BGC BGC 0.8836
121 7G1 0.8836
122 6J3 0.8835
123 FPL 0.8835
124 7G0 0.8829
125 FT1 0.8829
126 A18 0.8827
127 LJ4 0.8823
128 Y70 0.8822
129 2L1 0.8822
130 GMP 0.8816
131 TPM 0.8814
132 0UL 0.8813
133 TGW 0.8810
134 0OO 0.8809
135 QC1 0.8808
136 272 0.8806
137 AOY 0.8804
138 5WK 0.8804
139 6SW 0.8804
140 SOJ 0.8802
141 C5Q 0.8801
142 92O 0.8799
143 A4V 0.8797
144 IMK 0.8797
145 JA3 0.8796
146 XYP AHR 0.8796
147 DBM 0.8796
148 EAT 0.8795
149 F4U 0.8795
150 NEO 0.8795
151 MTP 0.8792
152 DBS 0.8791
153 MTA 0.8789
154 11X 0.8786
155 DS8 0.8785
156 16Z 0.8782
157 69K 0.8781
158 ESE 0.8781
159 7CH 0.8779
160 3F4 0.8778
161 5CQ 0.8776
162 SZ5 0.8776
163 MJ5 0.8775
164 FT2 0.8770
165 KWB 0.8769
166 RE4 0.8768
167 C0H 0.8767
168 6BK 0.8767
169 HO6 0.8765
170 0QV 0.8765
171 25F 0.8763
172 AVX 0.8763
173 DZ1 0.8762
174 L2K 0.8761
175 MQ1 0.8759
176 AHR AHR 0.8756
177 NAL 0.8756
178 C2M 0.8752
179 SP1 0.8752
180 GPK 0.8751
181 H4B 0.8750
182 LI4 0.8749
183 6DQ 0.8748
184 VJJ 0.8746
185 DTK 0.8744
186 F40 0.8743
187 ERZ 0.8742
188 GFE 0.8742
189 B1T 0.8742
190 4CN 0.8740
191 3WK 0.8740
192 1FL 0.8739
193 NPZ 0.8737
194 BMC 0.8736
195 MXD 0.8734
196 5R9 0.8733
197 KUP 0.8730
198 RGK 0.8729
199 4Z1 0.8727
200 H7S 0.8726
201 DK4 0.8726
202 5S9 0.8724
203 A7Q 0.8722
204 MJW 0.8719
205 JFZ 0.8719
206 4YE 0.8718
207 2L2 0.8717
208 4NR 0.8716
209 AX8 0.8716
210 B5A 0.8715
211 LR2 0.8714
212 LU2 0.8713
213 TH1 0.8713
214 CUH 0.8712
215 51Y 0.8711
216 BG8 0.8711
217 H75 0.8708
218 CL9 0.8707
219 4MP 0.8705
220 NQ7 0.8705
221 5E4 0.8696
222 6SY 0.8696
223 9CE 0.8695
224 CC7 0.8694
225 M3W 0.8692
226 28A 0.8687
227 BDJ 0.8686
228 A8S 0.8685
229 MG7 0.8684
230 DGO MAN 0.8684
231 TOP 0.8681
232 GZV 0.8681
233 X2M 0.8681
234 5M2 0.8680
235 JOB 0.8680
236 2P3 0.8678
237 DE7 0.8677
238 64I 0.8676
239 NOJ BGC 0.8675
240 H2B 0.8675
241 JFS 0.8674
242 S0D 0.8674
243 KHP 0.8669
244 SA0 0.8668
245 B4L 0.8668
246 1SF 0.8668
247 NKI 0.8667
248 EQW 0.8667
249 CH8 0.8667
250 2JX 0.8664
251 8OE 0.8664
252 J47 0.8662
253 PW1 0.8661
254 A6H 0.8660
255 26A 0.8660
256 PCG 0.8659
257 42R 0.8659
258 4EU 0.8656
259 X29 0.8653
260 JO5 0.8653
261 GLC BGC 0.8652
262 IEE 0.8651
263 7FZ 0.8651
264 A4N 0.8650
265 CHJ 0.8649
266 VT3 0.8644
267 GNG 0.8643
268 27M 0.8642
269 CTE 0.8642
270 TIA 0.8640
271 GAT 0.8636
272 4AF 0.8635
273 4WF 0.8631
274 AYS 0.8629
275 68B 0.8628
276 M2E 0.8628
277 26C 0.8627
278 9FG 0.8623
279 DKZ 0.8621
280 KW7 0.8621
281 L3L 0.8619
282 HBI 0.8619
283 C6Z 0.8618
284 EDG AHR 0.8618
285 MQR 0.8614
286 14N 0.8614
287 0ON 0.8610
288 DKX 0.8608
289 2QU 0.8607
290 JF8 0.8606
291 AGI 0.8605
292 MZR 0.8605
293 E9P 0.8604
294 0OP 0.8604
295 KMP 0.8603
296 2PV 0.8602
297 OSP 0.8602
298 2PK 0.8601
299 5VU 0.8599
300 NIY 0.8598
301 BGC GAL 0.8598
302 1A5 0.8597
303 54F 0.8595
304 CUQ 0.8594
305 SJK 0.8591
306 BC3 0.8591
307 GEN 0.8587
308 C93 0.8581
309 GPU 0.8581
310 M77 0.8578
311 CJB 0.8578
312 NXY 0.8575
313 GLC GAL 0.8575
314 VIB 0.8574
315 BBY 0.8571
316 AWE 0.8569
317 5NB 0.8567
318 A8K 0.8566
319 HX8 0.8562
320 35G 0.8560
321 GPQ 0.8558
322 3AK 0.8554
323 STZ 0.8546
324 EES 0.8538
325 AP6 0.8537
326 SX3 0.8536
327 5F7 0.8528
328 NEU 0.8525
329 TMG 0.8524
330 GJG 0.8519
331 3SU 0.8516
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1VBR; Ligand: XYP XYS; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 1vbr.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 4PMZ XYP XYP 42.5743
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