Receptor
PDB id Resolution Class Description Source Keywords
4D1J 1.8 Å EC: 3.2.1.23 THE STRUCTURE OF THE GH35 BETA-GALACTOSIDASE BGL35A FROM CELLVIBRIO JAPONICAS IN COMPLEX WITH 1- D EOXYGALACTONOJIRIMYCIN CELLVIBRIO JAPONICUS HYDROLASE ENZYME-CARBOHYDRATE INTERACTION GLYCOSIDASE INHI
Ref.: A COMPLEX GENE LOCUS ENABLES XYLOGLUCAN UTILIZATION MODEL SAPROPHYTE CELLVIBRIO JAPONICUS. MOL.MICROBIOL. V. 94 418 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT C:602;
D:606;
F:605;
C:601;
D:605;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
DGJ E:600;
D:600;
B:600;
A:600;
H:600;
G:600;
C:600;
F:600;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
Kd = 485 nM
163.172 C6 H13 N O4 C1[C@...
NA E:603;
F:604;
D:601;
G:603;
G:601;
E:602;
F:602;
H:601;
F:603;
E:601;
B:602;
D:604;
D:602;
B:601;
A:602;
E:604;
G:604;
A:601;
F:601;
A:603;
A:604;
G:602;
D:603;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4D1J 1.8 Å EC: 3.2.1.23 THE STRUCTURE OF THE GH35 BETA-GALACTOSIDASE BGL35A FROM CELLVIBRIO JAPONICAS IN COMPLEX WITH 1- D EOXYGALACTONOJIRIMYCIN CELLVIBRIO JAPONICUS HYDROLASE ENZYME-CARBOHYDRATE INTERACTION GLYCOSIDASE INHI
Ref.: A COMPLEX GENE LOCUS ENABLES XYLOGLUCAN UTILIZATION MODEL SAPROPHYTE CELLVIBRIO JAPONICUS. MOL.MICROBIOL. V. 94 418 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 4D1J Kd = 485 nM DGJ C6 H13 N O4 C1[C@@H]([....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4D1J Kd = 485 nM DGJ C6 H13 N O4 C1[C@@H]([....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4D1J Kd = 485 nM DGJ C6 H13 N O4 C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DGJ; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 DGJ 1 1
2 NOJ 1 1
3 DMJ 1 1
4 IMR 0.703704 0.853659
5 EDG 0.703704 0.853659
6 1AB 0.703704 0.853659
7 LDU 0.703704 0.853659
8 HQ6 0.454545 0.765957
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: 91
This union binding pocket(no: 1) in the query (biounit: 4d1j.bio4) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2E0P CTT 0.0007178 0.47542 1.54143
2 2VOT NHV 0.0006989 0.40266 1.66667
3 3WV6 GAL GLC 0.0004346 0.46399 1.68919
4 3WV6 GAL BGC 0.001132 0.45114 1.68919
5 4EAY CS2 0.007817 0.42223 1.69082
6 3AYS CT3 0.0003388 0.48365 1.8617
7 2E40 LGC 0.0005262 0.45354 1.93548
8 2OD9 A1R NCA 0.04521 0.40148 1.94805
9 4JIE BMA 0.001913 0.43888 2.18688
10 4OKZ 3E9 0.03755 0.4005 2.19178
11 1M13 HYF 0.01995 0.42217 2.21519
12 4B0T ADP 0.01781 0.41419 2.23124
13 5AYI BGC 0.000761 0.43666 2.407
14 2H7C COA 0.03436 0.42902 2.40741
15 1OGO BGC GLC 0.008629 0.4086 2.40741
16 5F3I 5UJ 0.03153 0.4088 2.5
17 5GNX BGC 0.001028 0.43957 2.56959
18 3CMJ SRT 0.0004546 0.46401 2.58065
19 4YZT BGC BGC BGC BGC 0.0005242 0.42387 2.79851
20 3II1 BGC 0.000009848 0.55721 2.80374
21 5EOB 5QQ 0.04783 0.41388 2.82132
22 1TB3 FMN 0.02412 0.41692 2.84091
23 3NV3 GAL NAG MAN 0.001293 0.40545 2.89855
24 1ZB6 GST 0.01339 0.42638 2.9316
25 1ZB6 DIN 0.01269 0.42638 2.9316
26 3ZMR GLO BGC BGC XYS BGC XYS XYS 0.001327 0.40463 2.94737
27 2UVF AD0 0.01506 0.4001 2.96296
28 3GNP SOG 0.0006928 0.47636 3.07377
29 5H9Q TD2 0.0005686 0.45988 3.22581
30 4PSB GA3 0.01785 0.42498 3.22581
31 5FYR INS 0.007237 0.41527 3.3557
32 1DB1 VDX 0.03875 0.40512 3.4749
33 4UFH GIF 0.006069 0.42013 3.51682
34 2Z8G GLC GLC BGC 0.01704 0.40776 3.51852
35 2H8H H8H 0.01405 0.4118 3.5514
36 4GJ3 0XP 0.02216 0.41704 3.64238
37 1SLT NDG GAL 0.003203 0.40233 3.73134
38 1ZM1 BGC BGC BGC 0.01572 0.40432 3.73444
39 5H4R CTT 0.0002188 0.43978 3.78788
40 2VRQ XYP XYP AHR 0.001405 0.4631 3.83065
41 3GKJ HC3 0.02445 0.40613 3.87931
42 4HIA FMN 0.04091 0.40501 3.97727
43 1KKR 2AS 0.01173 0.40186 4.11622
44 1J3R 6PG 0.01242 0.40878 4.21053
45 3GCZ SAM 0.02296 0.40753 4.25532
46 5JSD ACY 1GN GAL 1GN BGC ACY GAL BGC 0.03493 0.41519 4.44444
47 1A78 TDG 0.001176 0.42208 4.47761
48 2OVW CBI 0.0006165 0.44074 4.62287
49 3OIX FMN 0.02226 0.40693 4.63768
50 4PVR ASP 0.01696 0.40701 4.83871
51 4PTX BGC 0.0009022 0.40143 4.86726
52 1QKQ MAN 0.002429 0.41504 4.92958
53 3PTQ NFG 0.000838 0.40188 4.9505
54 1ZOA 140 0.04569 0.40517 5.074
55 1FH8 XYP XIF 0.003547 0.42859 5.12821
56 1W6P NDG GAL 0.0006471 0.45099 5.22388
57 1GZW GAL BGC 0.001495 0.44437 5.22388
58 1W6O LAT 0.002217 0.44153 5.22388
59 1W6M GAL 0.0002516 0.40231 5.22388
60 2YMZ LAT 0.0001402 0.48503 5.38462
61 5L7G 6QE 0.02066 0.41369 5.57377
62 4M82 NGB 0.003101 0.45242 5.76441
63 1X0P FAD 0.005398 0.43298 6.29371
64 4ITM ATP 0.03099 0.40102 6.34921
65 4H2V AMP 0.01459 0.41826 6.36364
66 1CEN BGC BGC 0.008954 0.40688 6.41399
67 3WUC GLC GAL 0.02437 0.4081 6.56934
68 1B3X XYP XYP XYP 0.005233 0.42513 6.62252
69 5DG2 GAL GLC 0.000703 0.4587 6.66667
70 5JNN 6LM 0.009412 0.42995 6.84211
71 1WHT BZS 0.006875 0.40923 7.18954
72 1Z4O GL1 0.01592 0.40641 7.23982
73 2NYR SVR 0.02605 0.41263 7.38007
74 3VV1 GAL FUC 0.0007882 0.42991 7.5
75 4NBW NAD 0.02775 0.40966 8.56031
76 3QP8 HL0 0.01696 0.40508 8.69565
77 4UTW RFW 0.01887 0.40258 8.73362
78 1IS3 LAT 0.002236 0.42226 8.88889
79 1Y0G 8PP 0.04426 0.41046 8.90052
80 1OJK GLC BGC 0.001397 0.44763 8.95522
81 1OJJ GLC GAL 0.001605 0.4171 8.95522
82 5D4Y BXP 0.004735 0.40276 9.29577
83 1PX8 XYP 0.0004071 0.47503 11.4
84 1R87 XYP XYP XYP 0.008377 0.41712 12.4011
85 4WVW SLT 0.002137 0.43142 12.5
86 4PBG BGP 0.00106 0.42164 14.9573
87 3NZ1 3NY 0.006837 0.40444 16.092
88 5U98 1KX 0.03224 0.41642 16.1616
89 1LTT GAL BGC 0.003318 0.40746 19.5122
90 3QF7 ANP 0.03287 0.40856 32
91 5E7V M7E 0.01771 0.42082 46.6667
Pocket No.: 2; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: 10
This union binding pocket(no: 2) in the query (biounit: 4d1j.bio2) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2HFK E4H 0.01407 0.40251 2.82132
2 3ZXE PGZ 0.006195 0.41882 3.7594
3 3AGC RCC 0.03744 0.40359 4.71014
4 2P1C GG3 0.03966 0.40016 4.87179
5 1EOM NAG MAN MAN MAN NAG GAL NAG GAL 0.02115 0.40405 5.17241
6 5NFB 8VT 0.002835 0.41736 9.09091
7 4NG2 OHN 0.0229 0.40661 10.3261
8 3KRB NAP 0.02861 0.4132 10.479
9 4COL DTP 0.006121 0.43346 11.6667
10 1FM9 570 0.03312 0.40854 28
Pocket No.: 3; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: 9
This union binding pocket(no: 3) in the query (biounit: 4d1j.bio6) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5MW8 ATP 0.004283 0.44381 2.12314
2 4R33 SAH 0.04897 0.40194 2.14286
3 4R33 TRP 0.04897 0.40194 2.14286
4 4RNV HBA 0.03664 0.41203 2.5
5 3MF2 AMP 0.01622 0.41695 3.17919
6 4J7Q B7N 0.03302 0.40018 4.2042
7 2J3M PRI 0.0171 0.41474 5
8 1GQG DCD 0.02123 0.40883 8.57143
9 3MN5 LAB 0.01129 0.40628 21.0526
Pocket No.: 4; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: 12
This union binding pocket(no: 4) in the query (biounit: 4d1j.bio10) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3ETH ATP 0.01847 0.41071 1.97183
2 4GCZ FMN 0.008924 0.42342 2.33766
3 5DO8 BGC 0.01264 0.40005 2.40741
4 1OTH PAO 0.02555 0.40176 2.80374
5 3OBT SLB 0.004902 0.41095 3.91705
6 5DV2 C5P 0.02585 0.4015 4.0201
7 2W5F XYP XYP XYP 0.01053 0.40393 5.18518
8 4LAX FK5 0.006178 0.41518 5.20446
9 1RPJ ALL 0.01039 0.4042 6.25
10 2DIO EOD 0.01289 0.40934 10.1064
11 2Y8L ADP 0.02454 0.43373 10.3448
12 3IS2 FAD 0.0113 0.43075 14.9351
Pocket No.: 5; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 4d1j.bio10) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 4d1j.bio10) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 4d1j.bio10) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 4d1j.bio8) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: 5
This union binding pocket(no: 9) in the query (biounit: 4d1j.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2W62 BGC BGC BGC BGC BGC 0.04455 0.40804 2.03704
2 3JRS A8S 0.006333 0.43655 2.40385
3 4ER2 IVA VAL VAL STA ALA STA 0.02626 0.42163 5.15152
4 1MJJ HAL 0.03262 0.40015 5.47945
5 4TMK T5A 0.04846 0.40188 7.51174
Pocket No.: 10; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 4d1j.bio3) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 4d1j.bio5) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 4d1j.bio7) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 13; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: 2
This union binding pocket(no: 13) in the query (biounit: 4d1j.bio9) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3VNM SDD 0.02313 0.40046 5.46075
2 5DJT FMN 0.02428 0.40119 13.1148
Pocket No.: 14; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 14) in the query (biounit: 4d1j.bio9) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 15; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 15) in the query (biounit: 4d1j.bio9) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 16; Query (leader) PDB : 4D1J; Ligand: DGJ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 16) in the query (biounit: 4d1j.bio9) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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