Receptor
PDB id Resolution Class Description Source Keywords
3QXV 2.5 Å NON-ENZYME: OTHER STRUCTURE OF AN ANTI-METHOTREXATE CDR1-4 GRAFT VHH ANTIBODY WITH METHOTREXATE LAMA GLAMA CAMELID SINGLE DOMAIN ANTIBODY HEAVY CHAIN ONLY VHH ANTIBANTI-HAPTEN ANTIBODY CDRHAPTEN BINDING SMALL MOLECULE SELIGAND BINDING LOW MOLECULAR WEIGHT COMPOUND METHOTREXATESYSTEM
Ref.: AN ANTI-HAPTEN CAMELID ANTIBODY REVEALS A CRYPTIC B SITE WITH SIGNIFICANT ENERGETIC CONTRIBUTIONS FROM NONHYPERVARIABLE LOOP. PROTEIN SCI. V. 20 1196 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MTX A:2000;
B:2000;
C:2000;
D:2000;
E:2000;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
Kd = 5 nM
454.439 C20 H22 N8 O5 CN(Cc...
SO4 A:3000;
B:3000;
B:3001;
C:3000;
Invalid;
Invalid;
Invalid;
Invalid;
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
3QXV 2.5 Å NON-ENZYME: OTHER STRUCTURE OF AN ANTI-METHOTREXATE CDR1-4 GRAFT VHH ANTIBODY WITH METHOTREXATE LAMA GLAMA CAMELID SINGLE DOMAIN ANTIBODY HEAVY CHAIN ONLY VHH ANTIBANTI-HAPTEN ANTIBODY CDRHAPTEN BINDING SMALL MOLECULE SELIGAND BINDING LOW MOLECULAR WEIGHT COMPOUND METHOTREXATESYSTEM
Ref.: AN ANTI-HAPTEN CAMELID ANTIBODY REVEALS A CRYPTIC B SITE WITH SIGNIFICANT ENERGETIC CONTRIBUTIONS FROM NONHYPERVARIABLE LOOP. PROTEIN SCI. V. 20 1196 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 3QXT Kd = 6700 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
2 3QXV Kd = 5 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 65 families.
1 1QD0 - RR6 C35 H25 N9 O22 S6 c1cc(c(cc1....
2 1I3U - RR1 C19 H16 N8 O10 S3 c1ccc(c(c1....
3 3QXT Kd = 6700 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
4 3QXV Kd = 5 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
5 2X6M - GLY TYR GLN ASP TYR GLU PRO GLU ALA n/a n/a
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 families.
1 1QD0 - RR6 C35 H25 N9 O22 S6 c1cc(c(cc1....
2 1I3U - RR1 C19 H16 N8 O10 S3 c1ccc(c(c1....
3 3LN9 - FLC C6 H5 O7 C(C(=O)[O-....
4 3QXT Kd = 6700 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
5 3QXV Kd = 5 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
6 2X6M - GLY TYR GLN ASP TYR GLU PRO GLU ALA n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MTX; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 MTX 1 1
2 3BI 0.783505 0.884058
3 2MX 0.778947 0.924242
4 04J 0.663043 0.870968
5 MT1 0.632653 0.968254
6 MOT 0.534653 0.923077
7 COP 0.453782 0.815385
8 FOL 0.410714 0.779412
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3QXV; Ligand: MTX; Similar sites found: 72
This union binding pocket(no: 1) in the query (biounit: 3qxv.bio2) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4DSU BZI 0.00006901 0.53628 None
2 5CLO NS8 0.0004268 0.49088 None
3 1MFI FHC 0.003822 0.445 None
4 4AGQ P96 0.0009794 0.43232 None
5 5MX4 HPA 0.00885 0.42353 None
6 2Y7P SAL 0.01012 0.41874 None
7 1V3S ATP 0.001736 0.4139 None
8 4RQL SNE 0.01067 0.41293 None
9 3ZF8 GDP 0.009878 0.41021 None
10 3GXW SIN 0.004252 0.40285 None
11 3G89 SAM 0.01082 0.40042 None
12 5FUI APY 0.0022 0.43626 1.5873
13 1ZNY GDP 0.005686 0.43141 1.5873
14 3ESS 18N 0.01395 0.41588 1.5873
15 4ZTD ALA GLY ALA GLY ALA 0.0009852 0.47744 2.38095
16 1VMK GUN 0.005646 0.43224 2.38095
17 5HWV MBN 0.006508 0.42844 2.38095
18 3VKX T3 0.0005947 0.413 2.38095
19 4L3L 5FI 0.01059 0.40962 2.38095
20 2WZ5 MET 0.003996 0.40132 2.38095
21 3IWD M2T 0.0172 0.40702 2.94118
22 1SBR VIB 0.01068 0.41754 3.1746
23 1UPR 4IP 0.01144 0.43051 3.25203
24 4KBA 1QM 0.003567 0.43639 3.96825
25 3O9L LPN 0.02659 0.40166 3.96825
26 3CM2 X23 0.02559 0.40124 3.96825
27 3A16 PXO 0.0009412 0.48051 4.7619
28 3CBC DBS 0.001061 0.47233 4.7619
29 1XXR MAN 0.002517 0.44608 4.7619
30 3TW1 AHN 0.003526 0.44398 4.7619
31 1GG6 APL 0.005656 0.42627 4.7619
32 5TH5 MET 0.008087 0.42366 4.7619
33 2WEL K88 0.01225 0.41757 4.7619
34 1BZL FAD 0.04719 0.4174 4.7619
35 2Z9I GLY ALA THR VAL 0.01353 0.41144 4.7619
36 3E7O 35F 0.01521 0.40481 4.7619
37 1NME 159 0.04214 0.40342 4.7619
38 5KJW 53C 0.0005455 0.48386 5.55556
39 1LSH PLD 0.001877 0.4442 5.55556
40 2XG5 EC2 0.008781 0.42928 5.55556
41 2XG5 EC5 0.008781 0.42928 5.55556
42 3UOY NAP 0.04967 0.40502 5.55556
43 1UYY BGC BGC 0.02084 0.40277 5.55556
44 4FFG 0U8 0.005827 0.45005 6.34921
45 4IXW IXW 0.005269 0.42805 6.34921
46 3AI3 SOE 0.00684 0.42735 6.34921
47 3NZ1 3NY 0.01461 0.41886 6.34921
48 5H2U 1N1 0.005717 0.4092 6.34921
49 2MSB NAG BMA MAN MAN MAN MAN MAN 0.02123 0.40217 6.95652
50 5LXB 7A9 0.0236 0.40351 7.14286
51 4WOE ADP 0.0226 0.40138 7.14286
52 1HXD BTN 0.007359 0.40069 7.14286
53 1DRJ RIP 0.0226 0.40013 7.14286
54 1OFL NGK GCD 0.001582 0.45741 7.93651
55 1SES AMP 0.01188 0.41063 7.93651
56 2BKX F6R 0.01007 0.40185 7.93651
57 3ZJX BOG 0.008797 0.42224 8.73016
58 2RCU BUJ 0.02597 0.41181 8.73016
59 1K7V NAG GAL BGC 0.02752 0.41301 9.52381
60 4MOB ADP 0.001148 0.46862 10.3175
61 3KU0 ADE 0.01668 0.41538 10.3175
62 4EWN 0VR 0.00888 0.40064 11.1111
63 5F7J ADE 0.003878 0.44264 11.9048
64 2EB5 OXL 0.01609 0.4087 12.6984
65 4A0M NAD 0.01735 0.40444 13.4921
66 3I7V B4P 0.01367 0.41967 14.2857
67 3OV6 MK0 0.01148 0.40927 14.2857
68 3SAO DBH 0.0004388 0.49003 15.0794
69 3ITA AIC 0.003298 0.44258 15.0794
70 4C2W ANP 0.02451 0.4001 15.3846
71 1XX4 BAM 0.01503 0.41313 15.873
72 3MYZ TFX 0.04046 0.40375 18
Pocket No.: 2; Query (leader) PDB : 3QXV; Ligand: MTX; Similar sites found: 29
This union binding pocket(no: 2) in the query (biounit: 3qxv.bio3) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4FE2 AIR 0.009344 0.40723 None
2 1KGI T4A 0.01342 0.40471 None
3 4CNK FAD 0.03009 0.40429 None
4 2V3A FAD 0.03095 0.40367 1.5873
5 4XZ6 TMO 0.007483 0.40848 3.1746
6 3RAB GNP 0.01475 0.40428 3.1746
7 2WOX NDP 0.008159 0.42826 3.96825
8 4UCI ADN 0.02119 0.40878 3.96825
9 1O9P MLA 0.01487 0.40178 3.96825
10 4H2W 5GP 0.004567 0.40038 3.96825
11 3H0L ADP 0.01442 0.40244 4.7619
12 1A5Z FBP 0.01919 0.40078 4.7619
13 3E5P PPI 0.001042 0.42014 5.55556
14 2BJK NAD 0.02363 0.40555 5.55556
15 5FPE 3TR 0.003199 0.42663 7.14286
16 3T1A 5MA 0.007481 0.40971 7.14286
17 4IEN GDP 0.004677 0.4064 7.14286
18 2QIA U20 0.0152 0.41499 8.73016
19 3AD8 NAD 0.02223 0.40685 9.52381
20 3E9I XAH 0.01787 0.40571 10.3175
21 1BC5 ACE ASN TRP GLU THR PHE 0.009511 0.41126 11.1111
22 4PAB THG 0.009976 0.40204 11.1111
23 5UKL SIX 0.01613 0.40525 11.9048
24 4LH0 GLV 0.02947 0.40282 12.6984
25 5LRT ADP 0.01494 0.40401 14.2857
26 4BLW SAH 0.02032 0.40043 14.2857
27 4DQ2 BTX 0.02027 0.40306 18.254
28 1L0I PSR 0.01566 0.40527 20.5128
29 2CYC TYR 0.01985 0.40247 25.3968
Pocket No.: 3; Query (leader) PDB : 3QXV; Ligand: MTX; Similar sites found: 17
This union binding pocket(no: 3) in the query (biounit: 3qxv.bio5) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2YN4 39J 0.01964 0.40484 None
2 1C3X 8IG 0.02736 0.40159 None
3 5W10 CMP 0.005399 0.40032 None
4 3QSB 743 0.0149 0.40162 1.5873
5 3I9U DTU 0.01757 0.40276 2.38095
6 3IT7 TLA 0.02864 0.4008 2.38095
7 4NOS ITU 0.01933 0.40015 3.1746
8 3BMO AX4 0.01515 0.40963 3.96825
9 3E7S AT2 0.0207 0.4032 3.96825
10 5XLY C2E 0.004742 0.40903 4.7619
11 1RYD GLC 0.02078 0.40538 5.55556
12 3P2H NOO 0.007602 0.40008 5.55556
13 3A23 GAL 0.02314 0.40045 7.93651
14 2GQS C2R 0.01005 0.40188 9.52381
15 5TV6 PML 0.02315 0.40044 9.52381
16 5FAW CHT 0.01871 0.40516 11.1111
17 5L2R MLA 0.03258 0.40085 14.2857
Pocket No.: 4; Query (leader) PDB : 3QXV; Ligand: MTX; Similar sites found: 10
This union binding pocket(no: 4) in the query (biounit: 3qxv.bio4) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1QKQ MAN 0.00773 0.43901 None
2 1L5Y BEF 0.004935 0.40848 None
3 4CJN QNZ 0.01854 0.41029 3.1746
4 5LX6 78P 0.02186 0.40172 3.1746
5 3C3D FO1 0.01649 0.40669 4.7619
6 2TOH HBI 0.01949 0.40587 4.7619
7 1B09 PC 0.006878 0.42735 7.93651
8 3QPB URA 0.01495 0.41278 7.93651
9 5A0U CHT 0.01735 0.40248 7.93651
10 4L77 CNL 0.02043 0.40321 23.0159
Pocket No.: 5; Query (leader) PDB : 3QXV; Ligand: MTX; Similar sites found: 6
This union binding pocket(no: 5) in the query (biounit: 3qxv.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1MID LAP 0.01063 0.40869 None
2 4A91 GLU 0.01653 0.40676 3.1746
3 2F5Z FAD 0.03134 0.40168 5.55556
4 1RO7 CSF 0.01355 0.40062 6.34921
5 5VNF VAL THR SER VAL VAL 0.01768 0.40208 7.93651
6 2Z5Y HRM 0.01562 0.40475 12.6984
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