FAIRMol

Z56842317

Pose ID 9219 Compound 3315 Pose 411

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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand Z56842317
PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
32.0 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.40, Jaccard 0.30, H-bond role recall 0.00
Burial
67%
Hydrophobic fit
91%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes 36% of hydrophobic surface appears solvent-exposed (8/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.699 kcal/mol/HA) ✓ Good fit quality (FQ -6.52) ✓ Good H-bonds (5 bonds) ✓ Deep burial (67% SASA buried) ✓ Lipophilic contacts well-matched (91%) ✗ Very high strain energy (32.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-18.882
kcal/mol
LE
-0.699
kcal/mol/HA
Fit Quality
-6.52
FQ (Leeson)
HAC
27
heavy atoms
MW
358
Da
LogP
3.96
cLogP
Strain ΔE
32.0 kcal/mol
SASA buried
67%
Lipo contact
91% BSA apolar/total
SASA unbound
626 Ų
Apolar buried
383 Ų

Interaction summary

HB 5 HY 9 PI 1 CLASH 6 ⚠ Exposure 36%

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
⚠️Partial hydrophobic solvent exposure
36% of hydrophobic surface appears solvent-exposed (8/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 22 Buried (contacted) 14 Exposed 8 LogP 3.96 H-bonds 5
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank3.608Score-18.882
Inter norm-0.828Intra norm0.128
Top1000noExcludedno
Contacts11H-bonds5
Artifact reasongeometry warning; 14 clashes; 1 protein clash; high strain Δ 32.0
Residues
ARG242 ARG337 ASP243 ASP385 GLU384 LEU339 MET386 PHE383 PRO338 TYR370 VAL336

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap6Native recall0.40
Jaccard0.30RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue1HB residue recall0.20

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:ORX602

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
421 2.9316708829612503 -0.946178 -23.0034 4 10 0 0.00 0.00 - no Open
506 2.983788791233104 -0.962875 -18.7321 6 15 0 0.00 0.00 - no Open
411 3.6075115201178534 -0.827665 -18.8819 5 11 6 0.40 0.00 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -18.882kcal/mol
Ligand efficiency (LE) -0.6993kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.524
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 358.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.96
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 74.74kcal/mol
Minimised FF energy 42.78kcal/mol

SASA & burial

✓ computed
SASA (unbound) 625.7Ų
Total solvent-accessible surface area of free ligand
BSA total 421.0Ų
Buried surface area upon binding
BSA apolar 383.1Ų
Hydrophobic contacts buried
BSA polar 37.8Ų
Polar contacts buried
Fraction buried 67.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 91.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2517.3Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1401.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)