FAIRMol

MK213

Pose ID 8334 Compound 534 Pose 204

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand MK213
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
25.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.79, Jaccard 0.68, H-bond role recall 0.57
Burial
76%
Hydrophobic fit
77%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.017 kcal/mol/HA) ✓ Good fit quality (FQ -9.81) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ High strain energy (25.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-30.514
kcal/mol
LE
-1.017
kcal/mol/HA
Fit Quality
-9.81
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
cLogP
Strain ΔE
25.2 kcal/mol
SASA buried
76%
Lipo contact
77% BSA apolar/total
SASA unbound
609 Ų
Apolar buried
358 Ų

Interaction summary

HB 11 HY 6 PI 4 CLASH 1

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank2.663Score-30.514
Inter norm-1.139Intra norm0.122
Top1000noExcludedno
Contacts18H-bonds11
Artifact reasongeometry warning; 13 clashes; 1 protein clash; moderate strain Δ 25.2
Residues
ALA67 ARG154 ARG277 ASP88 GLU274 GLY199 GLY201 GLY236 GLY237 GLY276 HIS197 LYS69 PHE170 PHE238 PRO275 SER200 TYR278 TYR389

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap15Native recall0.79
Jaccard0.68RMSD-
HB strict4Strict recall0.44
HB same residue+role4HB role recall0.57
HB same residue4HB residue recall0.57

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
263 1.0267699428225585 -1.16463 -31.7677 11 13 0 0.00 0.00 - no Open
248 1.0565759821753493 -1.05865 -27.2137 11 11 0 0.00 0.00 - no Open
275 1.158072578337196 -0.79049 -20.4723 4 16 0 0.00 0.00 - no Open
326 1.522628122716502 -0.968338 -25.9969 6 13 0 0.00 0.00 - no Open
244 1.708744967754064 -0.825708 -20.6159 5 19 0 0.00 0.00 - no Open
257 1.8345663825114074 -0.798505 -19.855 3 19 0 0.00 0.00 - no Open
309 1.905113599274035 -0.859805 -26.3343 3 12 0 0.00 0.00 - no Open
209 2.4824832058938013 -1.05337 -29.243 13 18 0 0.00 0.00 - no Open
204 2.663282674439042 -1.13906 -30.5138 11 18 15 0.79 0.57 - no Current
270 2.7066301048038337 -0.90359 -23.3047 8 16 0 0.00 0.00 - no Open
335 3.062936325722447 -0.858552 -27.4791 7 19 0 0.00 0.00 - no Open
224 3.0864929722424383 -0.941482 -26.4284 4 18 0 0.00 0.00 - no Open
308 3.1241016565923485 -1.04343 -27.852 6 10 0 0.00 0.00 - no Open
210 3.431812628247348 -1.01323 -26.2551 13 17 0 0.00 0.00 - no Open
200 4.283886601626247 -0.994469 -27.0487 13 17 0 0.00 0.00 - no Open
213 4.298392329825456 -0.999515 -28.3054 11 16 0 0.00 0.00 - no Open
307 4.451695165235262 -0.776336 -19.1475 5 13 0 0.00 0.00 - no Open
249 5.404412263953654 -0.824137 -19.6852 7 12 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -30.514kcal/mol
Ligand efficiency (LE) -1.0171kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.812
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.80
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 53.66kcal/mol
Minimised FF energy 28.47kcal/mol

SASA & burial

✓ computed
SASA (unbound) 608.6Ų
Total solvent-accessible surface area of free ligand
BSA total 464.7Ų
Buried surface area upon binding
BSA apolar 358.2Ų
Hydrophobic contacts buried
BSA polar 106.5Ų
Polar contacts buried
Fraction buried 76.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2561.8Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1388.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)