Receptor
PDB id Resolution Class Description Source Keywords
1UR9 1.8 Å EC: 3.2.1.14 INTERACTIONS OF A FAMILY 18 CHITINASE WITH THE DESIGNED INHI HM508, AND ITS DEGRADATION PRODUCT, CHITOBIONO-DELTA-LACTON SERRATIA MARCESCENS HYDROLASE CHITINASE INHIBITION LACTONE CHITIN DEGRADATION GLYCOSIDASE
Ref.: INTERACTIONS OF A FAMILY 18 CHITINASE WITH THE DESI INHIBITOR HM508 AND ITS DEGRADATION PRODUCT, CHITOB DELTA-LACTONE. J.BIOL.CHEM. V. 279 3612 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1500;
A:1501;
A:1502;
A:1503;
A:1504;
A:1505;
A:1506;
A:1507;
A:1508;
A:1509;
A:1510;
A:1511;
A:1512;
A:1513;
A:1514;
A:1515;
A:1516;
A:1517;
A:1518;
A:1519;
A:1520;
A:1521;
A:1522;
A:1523;
A:1524;
A:1525;
A:1526;
A:1527;
A:1528;
A:1529;
A:1538;
B:1500;
B:1501;
B:1502;
B:1503;
B:1504;
B:1505;
B:1506;
B:1507;
B:1508;
B:1509;
B:1510;
B:1511;
B:1512;
B:1513;
B:1514;
B:1515;
B:1516;
B:1517;
B:1518;
B:1519;
B:1520;
B:1521;
B:1522;
B:1523;
B:1524;
B:1525;
B:1526;
B:1527;
B:1528;
B:1529;
B:1530;
B:1531;
B:1537;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
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none;
submit data
92.094 C3 H8 O3 C(C(C...
NAG GDL PHJ A:2501;
B:2501;
Valid;
Valid;
none;
none;
Ki = 1.7 uM
556.525 n/a O(N=C...
SO4 A:1532;
A:1533;
A:1534;
A:1535;
A:1536;
A:1537;
B:1534;
B:1535;
B:1536;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3WD1 2.3 Å EC: 3.2.1.14 SERRATIA MARCESCENS CHITINASE B COMPLEXED WITH SYN-TRIAZOLE SERRATIA MARCESCENS TIM BARREL HYDROLASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: OBSERVATION OF THE CONTROLLED ASSEMBLY OF PRECLICK COMPONENTS IN THE IN SITU CLICK CHEMISTRY GENERATIO CHITINASE INHIBITOR PROC.NATL.ACAD.SCI.USA V. 110 15892 2013
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 3WD4 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
2 1UR9 Ki = 1.7 uM NAG GDL PHJ n/a n/a
3 1W1Y ic50 = 2.4 mM TYP C14 H16 N2 O3 c1cc(ccc1C....
4 1H0G - 0AR DPR UN2 HIS UN1 n/a n/a
5 1E6N - NAG NAG NAG NAG NAG n/a n/a
6 4Z2H ic50 = 8.3 uM M6A C33 H57 N5 O10 [H]/N=C(NC....
7 4Z2K - M6E C38 H67 N5 O10 [H]/N=C(/N....
8 3WD2 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
9 1E6Z - NAG NAG n/a n/a
10 1W1V ic50 = 6.3 mM ALJ C11 H19 N5 O2 C1C[C@H]2C....
11 3WD1 ic50 = 0.022 uM ST7 C37 H41 N11 O4 [H]/N=C(/N....
12 3WD3 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
13 1H0I - VR0 MEA IAS IAS DAL n/a n/a
14 1E6R - NAA NAA AMI n/a n/a
15 4Z2I ic50 = 0.036 uM M6B C34 H59 N5 O10 [H]/N=C(NC....
16 1O6I Ki = 0.65 mM 0HZ C11 H20 N5 O2 NULL
17 1W1P ic50 = 5 mM GIO C7 H10 N2 O2 C1C[C@H]2C....
18 1W1T ic50 = 1.1 mM CHQ C11 H14 N4 O2 c1c([nH]cn....
19 1UR8 Ki = 45 uM NAG GDL n/a n/a
20 4Z2L - M6F C31 H55 N5 O10 [H]/N=C(NC....
21 1OGG Ki = 6.4 uM NAA NAA AMI n/a n/a
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 3WD4 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
2 1UR9 Ki = 1.7 uM NAG GDL PHJ n/a n/a
3 1W1Y ic50 = 2.4 mM TYP C14 H16 N2 O3 c1cc(ccc1C....
4 1H0G - 0AR DPR UN2 HIS UN1 n/a n/a
5 1E6N - NAG NAG NAG NAG NAG n/a n/a
6 4Z2H ic50 = 8.3 uM M6A C33 H57 N5 O10 [H]/N=C(NC....
7 4Z2K - M6E C38 H67 N5 O10 [H]/N=C(/N....
8 3WD2 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
9 1E6Z - NAG NAG n/a n/a
10 1W1V ic50 = 6.3 mM ALJ C11 H19 N5 O2 C1C[C@H]2C....
11 3WD1 ic50 = 0.022 uM ST7 C37 H41 N11 O4 [H]/N=C(/N....
12 3WD3 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
13 1H0I - VR0 MEA IAS IAS DAL n/a n/a
14 1E6R - NAA NAA AMI n/a n/a
15 4Z2I ic50 = 0.036 uM M6B C34 H59 N5 O10 [H]/N=C(NC....
16 1O6I Ki = 0.65 mM 0HZ C11 H20 N5 O2 NULL
17 1W1P ic50 = 5 mM GIO C7 H10 N2 O2 C1C[C@H]2C....
18 1W1T ic50 = 1.1 mM CHQ C11 H14 N4 O2 c1c([nH]cn....
19 1UR8 Ki = 45 uM NAG GDL n/a n/a
20 4Z2L - M6F C31 H55 N5 O10 [H]/N=C(NC....
21 1OGG Ki = 6.4 uM NAA NAA AMI n/a n/a
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 3WD4 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
2 1UR9 Ki = 1.7 uM NAG GDL PHJ n/a n/a
3 1W1Y ic50 = 2.4 mM TYP C14 H16 N2 O3 c1cc(ccc1C....
4 1H0G - 0AR DPR UN2 HIS UN1 n/a n/a
5 1E6N - NAG NAG NAG NAG NAG n/a n/a
6 4Z2H ic50 = 8.3 uM M6A C33 H57 N5 O10 [H]/N=C(NC....
7 4Z2K - M6E C38 H67 N5 O10 [H]/N=C(/N....
8 3WD2 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
9 1E6Z - NAG NAG n/a n/a
10 1W1V ic50 = 6.3 mM ALJ C11 H19 N5 O2 C1C[C@H]2C....
11 3WD1 ic50 = 0.022 uM ST7 C37 H41 N11 O4 [H]/N=C(/N....
12 3WD3 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
13 1H0I - VR0 MEA IAS IAS DAL n/a n/a
14 1E6R - NAA NAA AMI n/a n/a
15 4Z2I ic50 = 0.036 uM M6B C34 H59 N5 O10 [H]/N=C(NC....
16 1O6I Ki = 0.65 mM 0HZ C11 H20 N5 O2 NULL
17 1W1P ic50 = 5 mM GIO C7 H10 N2 O2 C1C[C@H]2C....
18 1W1T ic50 = 1.1 mM CHQ C11 H14 N4 O2 c1c([nH]cn....
19 1UR8 Ki = 45 uM NAG GDL n/a n/a
20 4Z2L - M6F C31 H55 N5 O10 [H]/N=C(NC....
21 1OGG Ki = 6.4 uM NAA NAA AMI n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAG GDL PHJ; Similar ligands found: 39
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG GDL PHJ 1 1
2 OGN 0.622222 0.967213
3 OAN 0.622222 0.967213
4 5G0 GAL 0.542857 0.84058
5 NP6 0.504951 0.893939
6 8M7 0.504951 0.952381
7 VPU 0.490385 0.867647
8 MBG A2G 0.457447 0.741935
9 A2G MBG 0.457447 0.741935
10 CBS 0.431579 0.786885
11 NAG NDG 0.431579 0.786885
12 CBS CBS 0.431579 0.786885
13 NAG GDL 0.431579 0.786885
14 NGA GAL BGC 0.43 0.737705
15 NAG MBG 0.416667 0.741935
16 CTO 0.414141 0.803279
17 NAG NAG NAG NAG NDG NAG 0.414141 0.803279
18 NAG NAG NAG NAG NAG NAG NAG NAG 0.414141 0.803279
19 NAG NAG NDG 0.414141 0.803279
20 NDG NAG NAG NDG 0.414141 0.803279
21 NAG NAG NAG NAG 0.414141 0.803279
22 NDG NAG NAG 0.414141 0.803279
23 NAG NAG NAG NAG NAG NAG 0.414141 0.803279
24 NAG NAG 0.414141 0.723077
25 NDG NAG NAG NAG 0.414141 0.803279
26 NAG NAG NAG NDG 0.414141 0.803279
27 NAG NAG NAG 0.414141 0.803279
28 NAG NAG NAG NAG NDG 0.414141 0.803279
29 NDG NAG NAG NDG NAG 0.414141 0.803279
30 NAG NAG NAG NAG NAG 0.414141 0.803279
31 MAN NAG 0.410526 0.737705
32 NGA GAL 0.40625 0.737705
33 NAG GAL 0.40625 0.737705
34 GAL NAG 0.40625 0.737705
35 NAG A2G 0.402062 0.786885
36 NAG NGA 0.402062 0.786885
37 DLD 0.401869 0.75
38 NAG GAL BGC 0.4 0.737705
39 6Y2 0.4 0.838235
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3WD1; Ligand: ST7; Similar sites found: 10
This union binding pocket(no: 1) in the query (biounit: 3wd1.bio1) has 47 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5LOF MAL 0.04491 0.40626 1.78926
2 2W92 NGT 0.003552 0.47932 2.58449
3 3TTY GLA 0.0316 0.41815 2.98211
4 4UCF GLA 0.04784 0.40478 3.18091
5 4YG6 GAL NAG 0.04637 0.41284 4.90798
6 1EOM NAG MAN MAN MAN NAG GAL NAG GAL 0.004422 0.43925 8.27586
7 4NV1 TYD 0.03509 0.40602 10.6996
8 4P8X NAG NAG NAG NAG NAG NAG 0.00000001541 0.68036 44.7439
9 1NWU NAG NAG NAG NDG 0.0000000009211 0.71094 47.7901
10 2DT3 NAG NAG NAG NAG NAG NAG 0.00000001128 0.4623 48.7535
Pocket No.: 2; Query (leader) PDB : 3WD1; Ligand: ST7; Similar sites found: 165
This union binding pocket(no: 2) in the query (biounit: 3wd1.bio2) has 47 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO4 PIH 0.001018 0.52414 None
2 1UO5 PIH 0.02028 0.45882 None
3 4IHQ ADP 0.01324 0.42009 0.994036
4 1O9U ADZ 0.01965 0.44407 1.42857
5 3GTD MLI 0.01514 0.42667 1.65975
6 4J7H TRH 0.00393 0.41461 1.69851
7 4J7H TLO 0.007931 0.40024 1.69851
8 1C7S CBS 0.02023 0.40415 1.78926
9 4DYO SD4 0.02723 0.40609 1.85567
10 1Q11 TYE 0.01575 0.42113 1.88172
11 3E5P PPI 0.00129 0.54718 1.88679
12 3GM5 CIT 0.01373 0.43389 1.88679
13 1SS4 GSH 0.003779 0.50342 1.96078
14 1SS4 CIT 0.03398 0.44029 1.96078
15 2ZJ5 ADP 0.02383 0.41732 1.98807
16 1O0S NAI 0.003906 0.40505 1.98807
17 3SHR CMP 0.02639 0.40287 2.00669
18 2ZWS PLM 0.005683 0.49161 2.18688
19 3I8P 840 0.01632 0.40103 2.18688
20 3QV9 QV7 0.008554 0.4384 2.20441
21 1Y7P RIP 0.02099 0.42485 2.24215
22 2EB5 OXL 0.008758 0.44342 2.24719
23 2FEQ 34P 0.003252 0.42499 2.3166
24 3DER ALA LYS 0.003885 0.41143 2.31884
25 4B9E FAH 0.03101 0.42156 2.32558
26 1RZM E4P 0.01471 0.43803 2.36686
27 1RZM PEP 0.01605 0.42075 2.36686
28 3ZPG 5GP 0.008192 0.46478 2.38569
29 4JP3 CIT 0.01029 0.41652 2.51046
30 2IZ1 ATR 0.01541 0.43143 2.53165
31 2Z9V PXM 0.03556 0.40481 2.55102
32 3DGB MUC 0.01613 0.40831 2.6178
33 3ZF8 GDP 0.004369 0.43667 2.62295
34 1Z48 FMN 0.01489 0.40263 2.66272
35 4NAO AKG 0.01549 0.43689 2.76074
36 4E28 0MZ 0.01639 0.42504 2.76923
37 4E28 9MZ 0.04836 0.40695 2.76923
38 1GJW GLC 0.006741 0.45514 2.7833
39 1GJW MAL 0.01362 0.41534 2.7833
40 2ZB3 NDP 0.0007356 0.41367 2.7833
41 1EYE PMM 0.005535 0.42784 2.85714
42 3TFC PEP 0.01621 0.42056 2.85714
43 1MZV AMP 0.01055 0.42015 2.97872
44 2VDJ HSE 0.01179 0.4492 2.99003
45 1I0Z OXM 0.02588 0.43752 3.003
46 4KCT PYR 0.0136 0.41958 3.00601
47 4KCT FDP 0.0226 0.40211 3.00601
48 2ZJF BSU 0.003205 0.44247 3.03867
49 3E6J DR2 0.01358 0.45656 3.05677
50 3HB5 E2B 0.002111 0.41108 3.0581
51 1YOA FMN 0.004321 0.49865 3.14465
52 2VAR KDG 0.02309 0.40173 3.19489
53 3LTW HLZ 0.009329 0.44208 3.21429
54 2NVK NAP 0.03034 0.408 3.27869
55 1V6A TRE 0.01125 0.43278 3.31325
56 1QS8 IVA VAL VAL STA ALA STA 0.003764 0.4087 3.34347
57 3KMT SAH 0.006792 0.42006 3.36134
58 3OCZ SRA 0.007254 0.41148 3.37972
59 3S9K CIT 0.003088 0.52586 3.38983
60 2Q1A 2KT 0.005934 0.45167 3.41297
61 4EXO PYR 0.01399 0.44529 3.42466
62 2FR6 CTN 0.006459 0.40995 3.42466
63 2QF7 COA 0.01932 0.40145 3.51931
64 1NHZ 486 0.003948 0.40797 3.57143
65 1YHM AHD 0.01582 0.42577 3.59116
66 4JCA CIT 0.01623 0.45609 3.59281
67 4LHM AZZ 0.02818 0.41385 3.63636
68 2QLX RM4 0.01146 0.4435 3.7037
69 1PX8 XYP 0.01787 0.42326 3.8
70 1OGD RIP 0.014 0.42348 3.81679
71 1Y42 TYR 0.02185 0.41459 3.82653
72 1GEE NAD 0.001142 0.40496 3.83142
73 2YDW WSH 0.01888 0.40919 3.92157
74 1UJ2 C5P 0.001973 0.409 3.96825
75 1UJ2 ADP 0.001988 0.40889 3.96825
76 1ULE GLA GAL NAG 0.007603 0.45917 4
77 3UEC ALA ARG TPO LYS 0.03793 0.41709 4.10959
78 3I0O SMI 0.03384 0.41005 4.12979
79 1PEA ACM 0.01774 0.43988 4.15584
80 2W3L DRO 0.01176 0.45624 4.16667
81 1L8N GCW 0.005234 0.40067 4.17495
82 2QCX PF1 0.009117 0.43709 4.18251
83 2ZYF AKG 0.012 0.422 4.18848
84 3SIX GDP 0.01772 0.40659 4.24242
85 1G8S MET 0.02776 0.41888 4.34783
86 4L7I SAM 0.01097 0.40449 4.4226
87 3MAG 3MA 0.02857 0.44208 4.56026
88 3MAG SAH 0.007135 0.40504 4.56026
89 3P3N AKG 0.003906 0.46051 4.58453
90 2WA4 069 0.002662 0.44117 4.58453
91 2Y7P SAL 0.02465 0.41217 4.58716
92 4PTZ FMN 0.005285 0.41682 4.71204
93 2RHQ GAX 0.006281 0.40086 4.77137
94 4LN7 1ZQ 0.01144 0.40379 4.78469
95 2JFV FLC 0.02559 0.42062 4.811
96 1TH8 ADP 0.02004 0.40807 4.82759
97 1VE3 SAM 0.008811 0.40165 4.84582
98 3U1T MLI 0.04689 0.41235 4.85437
99 4COQ SAN 0.03049 0.41687 4.8583
100 1SQ5 PAU 0.004567 0.44576 4.87013
101 1Y2W NAG 0.01073 0.43912 4.92958
102 2OFE NAG 0.01097 0.43864 4.92958
103 3U7Y FLC 0.03179 0.44549 4.98615
104 3R51 MMA 0.02341 0.43991 5
105 2ORV 4TA 0.002196 0.41051 5.12821
106 1Y9Q MED 0.008291 0.44458 5.16899
107 5RHN 8BR 0.0009459 0.45026 5.21739
108 1JH7 UVC 0.04487 0.40417 5.29101
109 2YGO PCF 0.000696 0.41441 5.31915
110 4L6C 0BT 0.005329 0.40338 5.44554
111 2F2U M77 0.01224 0.41736 5.47264
112 3QDY A2G GAL 0.001558 0.49511 5.59441
113 3QDT A2G GAL 0.001788 0.49199 5.59441
114 3QDY CBS 0.002499 0.47685 5.59441
115 3GJB AKG 0.008456 0.42876 5.64263
116 2Q8H TF4 0.00681 0.46914 5.65111
117 3O2K DST 0.01025 0.42969 5.6962
118 3O2K QRP 0.0299 0.4005 5.6962
119 1Z4V DAN 0.01905 0.40526 5.76541
120 3EW2 BTN 0.0137 0.41943 5.92593
121 1GU3 BGC BGC BGC BGC BGC 0.04387 0.40056 6.04027
122 2C5S AMP 0.02643 0.40667 6.05327
123 2Q37 3AL 0.02492 0.41639 6.07735
124 1TFZ 869 0.007125 0.40506 6.16302
125 3TKA CTN 0.0009302 0.55724 6.34006
126 4M5P 23W 0.006802 0.4617 6.38821
127 4M5P MLA 0.03475 0.43721 6.38821
128 3CXQ GLP 0.01367 0.42877 6.52174
129 4M51 BEZ 0.026 0.43114 6.55738
130 1C1L GAL BGC 0.00934 0.448 6.56934
131 1BTN I3P 0.02951 0.45429 6.60377
132 1QO0 BMD 0.02568 0.42055 6.63265
133 1T0S BML 0.02755 0.42981 6.66667
134 1A4K FRA 0.03832 0.40746 6.84932
135 4F8L GAL 0.01009 0.47683 6.89655
136 2C2A ADP 0.007318 0.41133 7.36434
137 1XE7 GUN 0.001188 0.51026 7.38916
138 4K30 NLG 0.007647 0.43552 7.5
139 1Y1A GSH 0.01461 0.47364 7.65027
140 1V7R CIT 0.004521 0.48756 8.06452
141 1H8G CHT 0.006487 0.48821 8.42105
142 2R5T ANP 0.007258 0.40164 8.57909
143 1EB9 HBA 0.02394 0.40106 8.77863
144 4G4S LDZ 0.006845 0.41246 9.1954
145 1XX4 BAM 0.03081 0.4098 9.1954
146 3BHO B4P 0.01516 0.45778 9.61539
147 4RJK PYR 0.006022 0.46447 9.74155
148 3DG6 MUC 0.01925 0.40152 9.80926
149 2JGS BTN 0.03349 0.4081 10
150 2YLD CMO 0.02363 0.42232 10.2362
151 2BOI MFU 0.01254 0.42568 10.6195
152 2V5E SCR 0.01497 0.45809 10.8911
153 4BG1 IVL 0.00733 0.40148 11.3695
154 4BG1 OGA 0.00733 0.40148 11.3695
155 3W8S GSH 0.01492 0.42697 12.6214
156 2E1A MSE 0.01278 0.42078 13.3333
157 2WMO GTP 0.01937 0.4014 13.6842
158 1Y75 NAG 0.02901 0.40486 16.9492
159 3MD0 GDP 0.01932 0.41277 17.4648
160 1ECM TSA 0.01015 0.42523 18.3486
161 1N9L FMN 0.007835 0.40678 18.3486
162 3RF4 FUN 0.008598 0.43319 20.6897
163 1F5F DHT 0.01323 0.40133 25.3659
164 4CCO OGA 0.005346 0.44263 35
165 4F4S EFO 0.01581 0.42105 35.5263
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