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Receptor
PDB id Resolution Class Description Source Keywords
2QZ3 1.8 Å EC: 3.2.1.8 CRYSTAL STRUCTURE OF A GLYCOSIDE HYDROLASE FAMILY 11 XYLANASE FROM BACILLUS SUBTILIS IN COMPLEX WITH X YLOTETRAOSE BACILLUS SUBTILIS GLYCOSIDE HYDROLASE XYLANASE GLYCOSIDASE XYLAN DEGRADATION
Ref.: CRYSTALLOGRAPHIC ANALYSIS SHOWS SUBSTRATE BINDING AT THE -3 TO +1 ACTIVE-SITE SUBSITES AND AT THE SURFACE OF GLYCOSIDE HYDROLASE FAMILY 11 ENDO-1,4-BETA-XYLANASES. BIOCHEM.J. V. 410 71 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACY A:1022;
Invalid;
none;
submit data
60.052 C2 H4 O2 CC(=O...
XYP XYP XYP A:186;
A:189;
B:186;
B:189;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
414.36 n/a O(C1C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5TZO 1.67 Å EC: 3.2.1.8 COMPUTATIONALLY DESIGNED FENTANYL BINDER - FEN49*-COMPLEX BACILLUS SUBTILIS (STRAIN 168) COMPUTATIONAL DESIGN FENTANYL HYDROLASE
Ref.: COMPUTATIONAL DESIGN OF ENVIRONMENTAL SENSORS FOR T OPIOID FENTANYL. ELIFE V. 6 2017
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 1BCX - XYP XYP n/a n/a
2 5TZO Kd = 5.9 uM 7V7 C22 H28 N2 O CCC(=O)N(c....
3 2QZ3 - XYP XYP XYP n/a n/a
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 1BCX - XYP XYP n/a n/a
2 5TZO Kd = 5.9 uM 7V7 C22 H28 N2 O CCC(=O)N(c....
3 2QZ3 - XYP XYP XYP n/a n/a
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 3LGR - PDC C7 H5 N O4 c1cc(nc(c1....
2 4HK9 - XYP XYP XYP n/a n/a
3 4HK8 - XYP XYP XYP XYP XYP XYP n/a n/a
4 4HKW - XYP XYP TRS n/a n/a
5 2VGD - XYP XYP n/a n/a
6 1BCX - XYP XYP n/a n/a
7 5TZO Kd = 5.9 uM 7V7 C22 H28 N2 O CCC(=O)N(c....
8 2QZ3 - XYP XYP XYP n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: XYP XYP XYP; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 XYS XYS XYS XYS 1 1
2 XYP XYP XYP XYP 1 1
3 XYP XYP XYS 1 1
4 XYS XYS XYS XYS XYS 1 1
5 XYP XYP XYP XYP XYP XYP 1 1
6 XYP XYP XYP XYP XYP XYP XYP 1 1
7 XYS XYP XYP 1 1
8 XYP XYP XYP 1 1
9 XYP XYP XYP XYS 1 1
10 XYP XYS XYP 1 1
11 XYP XYP XYP XYP XYP 1 1
12 BXP 0.904762 1
13 XYS XYP 0.904762 1
14 XYP XYS 0.904762 1
15 XYS XYS XYS 0.791667 0.969697
16 XYP XYP XYP AHR 0.590909 0.888889
17 XYS XYP AHR XYP 0.590909 0.888889
18 XYP AHR XYP XYP 0.590909 0.888889
19 AHR XYP XYP XYP 0.575758 0.888889
20 AHR XYS XYP XYP XYP 0.560606 0.888889
21 XYS XYS 0.511111 0.939394
22 XYP XYP TRS 0.508197 0.711111
23 XYP XYP GCV XYP 0.506494 0.888889
24 XYS XYS AZI 0.5 0.653061
25 XYP XYP XYP GCV 0.493506 0.888889
26 GCV XYP XYP XYS 0.493506 0.888889
27 GCV XYP XYP XYP 0.493506 0.888889
28 AHR XYP XYP 0.484848 0.888889
29 XYP XYP AHR 0.484848 0.888889
30 XYS XYP AHR 0.484848 0.888889
31 AHR XYS XYS 0.484848 0.888889
32 XYS XYS NPO 0.455882 0.615385
33 XYP XDN 0.438596 0.704545
34 XIF XYP 0.438596 0.659574
35 XYP XIF 0.438596 0.659574
36 XDN XYP 0.438596 0.704545
37 GCV XYP XYP 0.415584 0.888889
38 GLC GLC XYP 0.405797 0.911765
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5TZO; Ligand: 7V7; Similar sites found with APoc: 183
This union binding pocket(no: 1) in the query (biounit: 5tzo.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 2YC5 6BC None
3 2UX9 FMN None
4 3STK PLM None
5 3W6X HZP 1.59574
6 1S4M LUM 1.59574
7 6D6L FY4 1.76471
8 5AYT L6Y 1.88679
9 1KOR SIN 2.12766
10 5FLJ QUE 2.15054
11 2P7Q GG6 2.25564
12 3TCT 3MI 2.3622
13 5F6U 5VK 2.54777
14 5FPX GLY SER SER HIS HIS HIS HIS HIS 2.65487
15 4FAJ LEU VAL THR LEU VAL PHE VAL 2.65957
16 5AE2 FYC 2.65957
17 5AE2 FAD 2.65957
18 3L9R L9R 2.65957
19 1RYD GLC 2.65957
20 4L3L 5FI 2.65957
21 6EK3 OUL 2.65957
22 3L9R L9Q 2.65957
23 5GP0 GPP 2.68456
24 1NFS DED 2.73224
25 2WSA MYA 3.19149
26 2WSA 646 3.19149
27 2VDF OCT 3.19149
28 2YNE NHW 3.19149
29 2YNE YNE 3.19149
30 6ALW BNV 3.19149
31 6ALW BMJ 3.19149
32 2RCU BUJ 3.19149
33 5KJW 53C 3.19149
34 4HWS 1B3 3.19149
35 3I3X U22 3.19149
36 4RKX 3S9 3.19149
37 5YXC CIT 3.19149
38 4HWT 1B2 3.19149
39 2OBD 2OB 3.19149
40 1Y0G 8PP 3.19149
41 1KRR ACO 3.19149
42 1RE8 BD2 3.19149
43 3PFG TLO 3.19149
44 3PFG SAM 3.19149
45 6CC0 EWM 3.19149
46 5W10 CMP 3.19149
47 4DXD 9PC 3.28283
48 5L2R MLA 3.7234
49 4F7E 0SH 3.7234
50 2C78 PUL 3.7234
51 3DLG GWE 3.7234
52 5BVE 4VG 3.7234
53 4D4U FUC NDG GAL FUC 3.7234
54 3VBK COA 3.7234
55 3EFS BTN 3.7234
56 3ACL 3F1 4.05405
57 2AZ5 307 4.05405
58 5O3Q CMP 4.16667
59 1OFL NGK GCD 4.25532
60 2QPU QPU 4.25532
61 2QPU QPS 4.25532
62 6FA4 D1W 4.25532
63 3A16 PXO 4.25532
64 2J3M PRI 4.25532
65 5MU6 MYA 4.25532
66 5MU6 KFK 4.25532
67 5OCG 9R5 4.25532
68 1NHX FTB 4.25532
69 1NHX PEP 4.25532
70 5DQ8 FLF 4.25532
71 5Y6Q MCN 4.25532
72 2XGT NSS 4.25532
73 5EJL C2E 4.25532
74 3LXK MI1 4.25532
75 4QAC KK3 4.25532
76 1TT8 PHB 4.26829
77 2GJ5 VD3 4.32099
78 5ANU 58T 4.43038
79 5XLY C2E 4.51128
80 2XOM GAL GAL GAL 4.60526
81 3MTX PGT 4.63576
82 5IXG OTP 4.73373
83 3QXV MTX 4.7619
84 2XCG XCG 4.78723
85 4MOB ADP 4.78723
86 4MOB COA 4.78723
87 1VPV PLM 4.78723
88 2QHV OC9 4.78723
89 2GTE VA 4.83871
90 2AG4 OLA 4.87805
91 2AG4 LP3 4.87805
92 3BJK CIT 5.22876
93 3WUR O4B 5.26316
94 4NV7 COA 5.31915
95 4B2Z P5S 5.31915
96 1XL8 OCB 5.31915
97 3UH0 TSB 5.31915
98 5LYH 7B8 5.31915
99 3E85 BSU 5.6962
100 3EM0 CHD 5.7971
101 1PZO CBT 5.85106
102 5LHT TIH 5.85106
103 4IGQ THR M3L GLN 5.85106
104 1LSH PLD 5.85106
105 4WO4 JLS 6
106 1OGA GLY ILE LEU GLY PHE VAL PHE THR LEU 6
107 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 6
108 5C0C ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA 6
109 5U98 1KX 6.06061
110 5WL1 CUY 6.06061
111 5WL1 D3D 6.06061
112 3HUJ AGH 6.06061
113 5IXH OTP 6.21118
114 5KWW 6YA 6.38298
115 3VET TOY 6.38298
116 3GNE FLC 6.38298
117 5J75 6GQ 6.38298
118 5TKJ ALA VAL GLY ILE GLY ALA VAL PHE 6.38298
119 5VAD 91Y 6.38298
120 2FTB OLA 6.4
121 6GNO XDI 6.66667
122 4YG6 GAL NAG 6.74847
123 5TUF TDC 6.91489
124 5TUF FAD 6.91489
125 5KD6 6C7 6.91489
126 3IU9 T07 6.91489
127 2IVD ACJ 6.91489
128 5TFZ 7BC 7.33333
129 2WLG SOP 7.44681
130 4B7P 9UN 7.44681
131 4Z87 GDP 7.44681
132 3ZPG 5GP 7.44681
133 5N2D 8J8 7.63889
134 2RHQ GAX 7.97872
135 5F3I 5UJ 7.97872
136 4O9S 2RY 7.97872
137 5IVE 6E8 7.97872
138 2JLD AG1 7.97872
139 6GH9 MIX 8.51064
140 4CS4 AXZ 8.51064
141 5NIU 8YZ 8.59375
142 5N2F 8HW 8.87097
143 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 9.04255
144 2JDR L20 9.04255
145 4WNK 453 9.04255
146 1LLU NAD 9.04255
147 3FYS PLM 9.57447
148 1SBR VIB 9.57447
149 5A89 FMN 9.61539
150 5A89 ADP 9.61539
151 5FUI APY 9.84848
152 1KJM ALA GLN PHE SER ALA SER ALA SER ARG 10
153 6DZN AE3 10.1064
154 5UKL SIX 10.1064
155 2YJ0 420 10.1449
156 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 10.2041
157 5LUN ARG 10.6383
158 5LUN OGA 10.6383
159 2QM9 TDZ 10.9677
160 4IEN GDP 11.0429
161 3TAY MN0 11.0429
162 4FL3 ANP 11.1702
163 2ZXI FAD 11.1702
164 5TSU CYS 11.7021
165 1KGI T4A 11.811
166 43CA NPO 11.9658
167 4GLW NMN 12.234
168 5FPE 3TR 12.234
169 4BVA T3 12.234
170 4XMF HSM 12.5
171 1D5Z ACE ALC ARG ALA ODA SER LEU NH2 14.3617
172 1JIF CU BLM 14.7541
173 4YLZ LAT NAG GAL 15.0327
174 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 15.7895
175 4DQ2 BTX 17.0213
176 3G08 FEE 17.1717
177 3RUG DB6 17.1717
178 5VC5 96M 18.617
179 1NYW DAU 19.1489
180 6DQU GLY ILE ILE ASN THR LEU 19.6809
181 5F7N NAG GAL FUC FUC A2G 20.8333
182 5F7Y GLC GAL NAG GAL FUC A2G 20.8333
183 1ZB6 GST 26.0638
Pocket No.: 2; Query (leader) PDB : 5TZO; Ligand: 7V7; Similar sites found with APoc: 139
This union binding pocket(no: 2) in the query (biounit: 5tzo.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 3T50 FMN None
2 4R38 RBF None
3 4CME KTZ 1.06383
4 1OVD ORO 2.12766
5 1OVD FMN 2.12766
6 4JH6 FCN 2.17391
7 3FW4 CAQ 2.24719
8 2Y6Q I7T 2.65957
9 2ZB4 NAP 2.65957
10 2ZB4 5OP 2.65957
11 5FM0 WAQ 2.65957
12 4FFS BIG 2.65957
13 1Q23 FUA 2.65957
14 3BXO UPP 2.65957
15 4BMX ADE 2.65957
16 2WSB NAD 2.65957
17 2VQ5 HBA 2.65957
18 5XFV FMN 2.65957
19 5Y72 DST 3.19149
20 6BYM HC3 3.19149
21 4WKC BIG 3.19149
22 2RDG NDG FUC SIA GAL 3.19149
23 4U0W 16G 3.19149
24 5X7Q GLC GLC GLC GLC GLC 3.7234
25 5TA6 79D 3.7234
26 5UGH 8AJ 3.7234
27 4L2I FAD 3.7234
28 4L2I NAD 3.7234
29 4TL6 ANP 3.7234
30 2JIG PD2 3.7234
31 1AJ0 SAN 3.7234
32 1AJ0 PH2 3.7234
33 4P25 FUC GAL NAG FUC 3.7234
34 2Z3U CRR 3.7234
35 3DGY 2GP 4.12371
36 2E56 MYR 4.16667
37 4LIT AKG 4.25532
38 2ZB3 NDP 4.25532
39 2ORV 4TA 4.25532
40 2X2M X2M 4.25532
41 4BHN BH9 4.25532
42 1EC9 XYH 4.25532
43 5HV0 AKG 4.25532
44 4TMC FMN 4.25532
45 4DXG NDG FUC SIA GAL 4.25532
46 4IE6 UN9 4.25532
47 1W4R TTP 4.25532
48 3I8T LBT 4.26829
49 3M3E GAL A2G NPO 4.34783
50 1QIN GIP 4.37158
51 4YHO 4CC 4.5045
52 5ML3 DL3 4.69799
53 2C1Q BTN 4.7619
54 1EWJ BLM 4.7619
55 3C3N FMN 4.78723
56 5GM5 CBI 4.78723
57 5CJF 520 4.78723
58 2R5V HHH 4.78723
59 4PNI KQQ 4.78723
60 3PB9 1BN 4.78723
61 4B7X NAP 4.78723
62 4MNS 2AX 5.03145
63 1V0C ACO 5.31915
64 4WKB TDI 5.31915
65 3KH5 ADP 5.31915
66 2HHJ 3PG 5.31915
67 2QRD ADP 5.31915
68 1MH5 HAL 5.31915
69 4NZF ARB 5.31915
70 4YZN 4K5 5.31915
71 2AXR ABL 5.31915
72 6GBV FMN 5.47945
73 3VQ2 LP4 LP5 MYR DAO 5.55556
74 1Y52 BTN 5.55556
75 3KPB SAM 5.7377
76 5C3R AKG 5.85106
77 5C3R HMU 5.85106
78 4YBN FAD 5.85106
79 3GPO APR 5.95238
80 5D3X 4IP 5.98802
81 3BRN SRO 6.36943
82 2YG2 FLC 6.39535
83 2YG2 S1P 6.39535
84 4BCS BTN 6.4
85 4WUJ FMN 6.80272
86 5KD6 LBU 6.91489
87 4K26 SFF 6.91489
88 6FXR AKG 6.91489
89 3CH6 311 6.91489
90 3CH6 NAP 6.91489
91 1YKD CMP 6.91489
92 2DM6 NAP 6.91489
93 4YGF AZM 6.91489
94 1XSE NDP 7.44681
95 1UNB PN1 7.44681
96 1UNB AKG 7.44681
97 5VZ0 ADP 7.44681
98 1UMZ BGC BGC XYS BGC XYS GAL 7.44681
99 1WBI BTN 7.75194
100 4WN5 MVC 7.82609
101 3EYA FAD 7.97872
102 5MZI FYK 7.97872
103 5MZI FAD 7.97872
104 5DRB 5FJ 7.97872
105 3GP3 SEP 7.97872
106 5YU3 NAD 8.51064
107 5YU3 PRO 8.51064
108 4RDL FUC GAL NDG FUC 8.51064
109 1OLM VTQ 8.51064
110 4RFR RHN 9.04255
111 1QFT HSM 9.14286
112 2HY0 306 9.57447
113 1YKJ FAD 10.1064
114 1YKJ PHB 10.1064
115 5G3U ITW 10.1064
116 5O9W AKG 10.1064
117 3VZS NAP 10.1064
118 5U75 SIA GAL NDG FUC 10.119
119 4RYV ZEA 10.9677
120 1N07 FMN 11.0429
121 5YVT NAI 11.1702
122 3ATY FMN 11.1702
123 1UW1 ADP 11.25
124 2TPI ILE VAL 12.069
125 4EUU BX7 12.234
126 4K3H 1OM 12.7119
127 4MLO PAM 12.766
128 3UA1 08Y 14.8936
129 3DWQ NGC GAL NGA POL AZI 15.0794
130 5YB7 FAD 15.4255
131 5YB7 ORN 15.4255
132 1ZOS MTM 16.4894
133 1LN1 DLP 17.0213
134 5TBM 79A 17.3913
135 3VPB ADP 17.5532
136 4NW6 2NS 17.5532
137 4COQ SAN 19.0283
138 1ZB6 DIN 26.0638
139 3E5A VX6 27.2727
Pocket No.: 3; Query (leader) PDB : 5TZO; Ligand: 7V7; Similar sites found with APoc: 22
This union binding pocket(no: 3) in the query (biounit: 5tzo.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 1Y7P RIP 2.65957
2 5L6G XYP 2.65957
3 3B6R CRN 3.19149
4 4FHD EEM 3.19149
5 4FHD 0TT 3.19149
6 5AIG VPR 3.2
7 4FFG LBS 3.7234
8 4MBY BGC SIA GAL 3.7234
9 1SDW IYT 3.7234
10 1OJK GLC BGC 4.25532
11 5JSP DQY 4.25532
12 1OJJ GLC GAL 4.25532
13 2GOO NDG 5.26316
14 4A34 FUL 9.52381
15 1N5S ADL 9.82143
16 6BU0 IHP 10.687
17 4JX1 CAH 11.7021
18 1RM0 D6P 11.7021
19 4M00 SUC 13.2979
20 3H7J PPY 15.9574
21 3HPY MCT 15.9574
22 5IVX ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 17
Pocket No.: 4; Query (leader) PDB : 5TZO; Ligand: 7V7; Similar sites found with APoc: 37
This union binding pocket(no: 4) in the query (biounit: 5tzo.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4P7U 1PS None
2 5CLO NS8 None
3 2XMY CDK 2.12766
4 4CJN QNZ 2.65957
5 4Z7X 3CX 2.65957
6 1EX7 5GP 2.68817
7 5E9G GLV 3.19149
8 2GU8 796 3.19149
9 5W0N UPU 3.19149
10 5N87 N66 3.7234
11 2X1E X1E 3.7234
12 3KYG 5GP 5GP 3.7234
13 2NNQ T4B 3.81679
14 3L5R 47X 4.09836
15 3KYF 5GP 5GP 4.25532
16 5LKC FUC GLA A2G 4.25532
17 6CDO ALA VAL GLY ILE GLY ALA VAL PHE 4.34783
18 3IAE D7K 4.78723
19 2G30 ALA ALA PHE 5.31915
20 1ZNY GDP 5.31915
21 3LKJ LKJ 5.67376
22 1WHT BZS 5.88235
23 3QFJ LEU LEU PHE GLY PHE PRO VAL TYR VAL 6
24 6BJ3 ILE PRO LEU THR GLU GLU ALA GLU LEU 6.06061
25 5VAD PRO 6.38298
26 5NKB 8ZT 6.38298
27 4MPO AMP 6.53595
28 4JLS 3ZE 6.57895
29 1OH2 SUC 6.91489
30 2Z81 PCJ 7.44681
31 6F5U CQN 7.97872
32 3A7R LAQ 7.97872
33 2VL1 GLY GLY 9.57447
34 2CJU PHX 9.91736
35 3O03 GCO 11.1702
36 5T96 79J 13.2979
37 4YVN EBS 14.8936
Pocket No.: 5; Query (leader) PDB : 5TZO; Ligand: 7V7; Similar sites found with APoc: 22
This union binding pocket(no: 5) in the query (biounit: 5tzo.bio3) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 5CCM SAM 2.65957
2 3TYZ PAB 2.65957
3 3TYZ XHP 2.65957
4 5XEG AKG 2.65957
5 3QP6 HL6 3.19149
6 5HES 032 3.19149
7 4HVA 4HV 3.7234
8 4X5S AZM 4.25532
9 3FW3 ETS 4.25532
10 3W21 AKG 5.31915
11 2PTZ PAH 5.85106
12 3O0Q TTP 5.85106
13 4XV1 904 6.38298
14 3NC9 TR3 6.38978
15 5DH3 5BS 6.91489
16 3GLC R5P 6.91489
17 4KGD TDP 7.44681
18 4KGD FAD 7.44681
19 1ERB ETR 7.65027
20 1S9D AFB 9.04255
21 1BZY IMU 10.1064
22 1NM5 NAP 10.6383
Pocket No.: 6; Query (leader) PDB : 5TZO; Ligand: 7V7; Similar sites found with APoc: 34
This union binding pocket(no: 6) in the query (biounit: 5tzo.bio3) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5XVG 8FX 2.12766
2 5CJ3 52G 2.22222
3 3NCQ ATP 2.52101
4 1VA6 ADP 2.65957
5 1KDK DHT 2.82486
6 5BYK A3P 3.19149
7 5BYK OAQ 3.19149
8 1GPM AMP 3.19149
9 2RDE C2E 3.7234
10 5JSD 1GN ACY GAL ACY 1GN BGC GAL BGC 3.7234
11 4R3U 3KK 4.25532
12 4R3U 3HC 4.25532
13 1F5F DHT 4.25532
14 1F9V ADP 4.78723
15 4RF7 ARG 4.78723
16 4XTX 590 5.92593
17 3SAO DBH 6.25
18 1FFU CDP 6.38298
19 5N5U 7N8 6.38298
20 4PFC 2QX 6.91489
21 2WZF BGC 6.91489
22 3DZ6 M8E 6.91489
23 3VCY UD1 7.44681
24 1T7Q 152 7.97872
25 1T7Q COA 7.97872
26 4CS4 ANP 8.51064
27 3LF0 ATP 9.64912
28 1WPY BTN 11.7021
29 2DXU BT5 12.234
30 3AD8 NAD 13.2979
31 1HXD BTN 14.8936
32 3SCM LGN 17.1717
33 1M5B BN1 19.1489
34 5FKP 6UL 22.7273
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