Receptor
PDB id Resolution Class Description Source Keywords
3mkj 1.65 Å EC: 4.4.1.11 METHIONINE GAMMA-LYASE FROM CITROBACTER FREUNDII WITH PYRIDO PHOSPHATE CITROBACTER FREUNDII PYRIDOXAL-5-prime -PHOSPHATE PLP-DEPENDENT ENZYME LYASE X-RAY D
Ref.: EXPLORING METHIONINE GAMMA-LYASE STRUCTURE-FUNCTION RELATIONSHIP VIA MICROSPECTROPHOTOMETRY AND X-RAY CRYSTALLOGRAPHY BIOCHIM.BIOPHYS.ACTA V.1814 834 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PZP A:399;
 Valid;
 none;
 submit data
246.157 C8 H11 N2 O5 P [H]/N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5M3Z 1.45 Å EC: 4.4.1.11 CRYSTAL STRUCTURE OF CITROBACTER FREUNDII METHIONINE GAMMA-L C115H REPLACEMENT IN THE COMPLEX WITH L-NORLEUCINE CITROBACTER FREUNDII METHIONINE GAMMA-LYASE C115H SUBSTITUTION L-NORLEUCINE LY
Ref.: CRYSTAL STRUCTURE OF MUTANT FORM CYS115HIS OF CITRO FREUNDII METHIONINE GAMMA-LYASE COMPLEXED WITH L-NO BIOCHIM. BIOPHYS. ACTA V.1865 1123 2017
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5M3Z Ki = 0.6 mM NLE C6 H13 N O2 CCCC[C@@H]....
2 4HF8 - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
3 3MKJ - PZP C8 H11 N2 O5 P [H]/N=C/c1....
4 4OMA - LCS C11 H14 N3 O7 P Cc1c(c(c(c....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3VK3 - MET C5 H11 N O2 S CSCC[C@@H]....
2 5X2X - 4LM C12 H15 N2 O7 P C/C=C(C(=O....
3 5X2Z - 3LM C13 H19 N2 O7 P S Cc1c(c(c(c....
4 5M3Z Ki = 0.6 mM NLE C6 H13 N O2 CCCC[C@@H]....
5 4HF8 - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
6 3MKJ - PZP C8 H11 N2 O5 P [H]/N=C/c1....
7 4OMA - LCS C11 H14 N3 O7 P Cc1c(c(c(c....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3VK3 - MET C5 H11 N O2 S CSCC[C@@H]....
2 5X2X - 4LM C12 H15 N2 O7 P C/C=C(C(=O....
3 5X2Z - 3LM C13 H19 N2 O7 P S Cc1c(c(c(c....
4 1E5F - PLP C8 H10 N O6 P Cc1c(c(c(c....
5 6NBA - P1T C11 H15 N2 O7 P Cc1c(c(c(c....
6 4IY7 - KOU C11 H15 N2 O8 P Cc1c(c(c(c....
7 5M3Z Ki = 0.6 mM NLE C6 H13 N O2 CCCC[C@@H]....
8 4HF8 - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
9 3MKJ - PZP C8 H11 N2 O5 P [H]/N=C/c1....
10 4OMA - LCS C11 H14 N3 O7 P Cc1c(c(c(c....
11 1CL2 - PPG C14 H20 N3 O8 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PZP; Similar ligands found: 64
No: Ligand ECFP6 Tc MDL keys Tc
1 PZP 1 1
2 PLP 0.729167 0.843137
3 AN7 0.59322 0.811321
4 EPC 0.59322 0.901961
5 0JO 0.590164 0.807018
6 EXT 0.583333 0.836364
7 FOO 0.583333 0.886792
8 PLR 0.568627 0.86
9 4LM 0.564516 0.821429
10 F0G 0.555556 0.867925
11 MPM 0.555556 0.851852
12 KOU 0.546875 0.839286
13 FEV 0.546875 0.807018
14 P3D 0.538462 0.79661
15 HCP 0.538462 0.807018
16 EVM 0.538462 0.824561
17 6DF 0.537313 0.884615
18 PXP 0.527273 0.830189
19 PMP 0.517857 0.836364
20 P0P 0.517857 0.88
21 PL6 0.514706 0.821429
22 GT1 0.508772 0.767857
23 PFM 0.507246 0.775862
24 Z98 0.507246 0.783333
25 FEJ 0.507246 0.854545
26 L7N 0.5 0.676056
27 P70 0.472973 0.836364
28 PUS 0.472973 0.712121
29 PL5 0.472973 0.810345
30 P89 0.460526 0.71875
31 EQJ 0.454545 0.758065
32 5DK 0.454545 0.758065
33 LUH 0.454545 0.716418
34 LUK 0.454545 0.716418
35 O1G 0.448718 0.783333
36 GLY PLP 0.441176 0.75
37 IN5 0.439394 0.793103
38 PLG 0.439394 0.754098
39 PLP PUT 0.43662 0.762712
40 Q0P 0.426829 0.79661
41 PLP ABU 0.424658 0.711864
42 PLP 999 0.424658 0.767857
43 C6P 0.422535 0.754098
44 PDD 0.42029 0.766667
45 P1T 0.42029 0.71875
46 PP3 0.42029 0.766667
47 PDA 0.42029 0.766667
48 PLT 0.416667 0.79661
49 SER PLP 0.416667 0.754386
50 IK2 0.414286 0.71875
51 33P 0.414286 0.779661
52 CKT 0.414286 0.79661
53 HEY 0.413333 0.707692
54 PLP ALO 0.410959 0.767857
55 TLP 0.408451 0.766667
56 PLS 0.408451 0.754098
57 2BO 0.408451 0.766667
58 PMH 0.408451 0.647887
59 5PA 0.408451 0.71875
60 2BK 0.408451 0.766667
61 PPD 0.402778 0.754098
62 DCS 0.4 0.621622
63 LPI 0.4 0.676471
64 LCS 0.4 0.652778
Similar Ligands (3D)
Ligand no: 1; Ligand: PZP; Similar ligands found: 178
No: Ligand Similarity coefficient
1 G6P 0.9676
2 4R1 0.9517
3 BG6 0.9515
4 GLP 0.9504
5 PLP PMP 0.9485
6 NPL 0.9420
7 1QV 0.9393
8 X04 0.9361
9 N2M 0.9349
10 A6P 0.9299
11 QIF 0.9263
12 MP5 0.9254
13 ZEC 0.9242
14 3LJ 0.9180
15 D6G 0.9177
16 68A 0.9165
17 6HP 0.9148
18 NAG 0.9146
19 5WN 0.9144
20 EVF 0.9118
21 BGP 0.9115
22 IOS 0.9095
23 SG2 0.9091
24 5OO 0.9081
25 F5C 0.9069
26 QMS 0.9068
27 IOP 0.9032
28 NBV 0.9026
29 BIO 0.9014
30 L21 0.9008
31 F06 0.9004
32 YF3 0.9000
33 CFA 0.8991
34 M6D 0.8984
35 F6P 0.8977
36 9BF 0.8970
37 HBI 0.8968
38 SBK 0.8967
39 ZHA 0.8954
40 4KR 0.8954
41 IPD 0.8948
42 F1P 0.8945
43 I2E 0.8942
44 KMY 0.8941
45 ABF 0.8927
46 IAC 0.8923
47 5TY 0.8914
48 ZON 0.8912
49 SG6 0.8911
50 61M 0.8907
51 TNX 0.8906
52 3RI 0.8904
53 ARP 0.8886
54 NFM 0.8883
55 TRP 0.8881
56 I4D 0.8881
57 AJD 0.8880
58 3VX 0.8878
59 F52 0.8877
60 FWD 0.8872
61 F1X 0.8871
62 S7G 0.8869
63 H4B 0.8862
64 AMR 0.8856
65 HSX 0.8849
66 SYE 0.8847
67 WV7 0.8843
68 GZV 0.8840
69 6J5 0.8837
70 ALX 0.8834
71 AKD 0.8833
72 KYN 0.8832
73 SKF 0.8832
74 EYV 0.8831
75 HWD 0.8829
76 ENG 0.8828
77 FER 0.8824
78 0FR 0.8817
79 ZEZ 0.8814
80 3Y7 0.8808
81 O2Y 0.8807
82 CTE 0.8805
83 2K8 0.8805
84 P2L 0.8799
85 LTM 0.8798
86 BEU 0.8792
87 TMG 0.8789
88 NPX 0.8789
89 5WM 0.8789
90 LP8 0.8788
91 BNX 0.8786
92 2HC 0.8785
93 TA6 0.8784
94 CHQ 0.8778
95 HBO 0.8776
96 MD6 0.8776
97 XIF XYP 0.8771
98 N91 0.8770
99 KF5 0.8768
100 X0T 0.8767
101 BQ2 0.8767
102 GB4 0.8766
103 CMU 0.8764
104 4WF 0.8763
105 H2B 0.8760
106 YO5 0.8759
107 657 0.8758
108 OSB 0.8755
109 EUH 0.8746
110 96Z 0.8745
111 4Z9 0.8744
112 3M8 0.8743
113 E9S 0.8743
114 3IL 0.8743
115 GO8 0.8741
116 XYP XIF 0.8733
117 4Z1 0.8733
118 DAH 0.8733
119 NGA 0.8732
120 4OG 0.8732
121 APS 0.8728
122 RVE 0.8728
123 0J5 0.8728
124 ZIP 0.8726
125 505 0.8725
126 TSR 0.8725
127 MQG 0.8724
128 9F8 0.8715
129 DTR 0.8714
130 DTE 0.8710
131 ZSP 0.8710
132 3IB 0.8710
133 FPL 0.8709
134 GXG 0.8708
135 1BW 0.8705
136 AVO 0.8704
137 D1Y 0.8697
138 PW1 0.8694
139 JF2 0.8690
140 SJK 0.8688
141 3SU 0.8685
142 NPA 0.8684
143 52F 0.8682
144 OIA 0.8676
145 7AP 0.8676
146 CC5 0.8675
147 A4V 0.8670
148 B41 0.8669
149 4AB 0.8668
150 EYY 0.8667
151 2VQ 0.8664
152 EV3 0.8660
153 3N1 0.8658
154 3JM 0.8656
155 S8A 0.8651
156 HPT 0.8651
157 MUX 0.8639
158 MJ5 0.8637
159 NAL 0.8633
160 ZEA 0.8629
161 GXD 0.8624
162 K82 0.8622
163 ITW 0.8621
164 K7H 0.8616
165 MBP 0.8614
166 TXW 0.8614
167 5WS 0.8609
168 7MX 0.8604
169 51Y 0.8603
170 PNP 0.8590
171 YOF 0.8588
172 NIY 0.8585
173 UQ1 0.8582
174 LTN 0.8578
175 5AD 0.8571
176 4NS 0.8565
177 GRX 0.8535
178 Q5M 0.8528
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5M3Z; Ligand: PLP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5m3z.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5M3Z; Ligand: PLP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5m3z.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5M3Z; Ligand: PLP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5m3z.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5M3Z; Ligand: PLP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5m3z.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5M3Z; Ligand: PY6; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5m3z.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5M3Z; Ligand: PY6; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5m3z.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5M3Z; Ligand: PY6; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5m3z.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5M3Z; Ligand: PY6; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5m3z.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 5M3Z; Ligand: NLE; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 5m3z.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 5M3Z; Ligand: NLE; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 5m3z.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 5M3Z; Ligand: NLE; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 5m3z.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 5M3Z; Ligand: NLE; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 5m3z.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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