FAIRMol

Z24314037

Pose ID 9272 Compound 2244 Pose 464

DB SELECTIONDocking 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 Z24314037
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 strong SASA done
Strain ΔE
30.7 kcal/mol
Protein clashes
0
Internal clashes
8
Native overlap
contact recall 0.60, Jaccard 0.38, H-bond role recall 0.40
Burial
82%
Hydrophobic fit
79%
Reason: 8 internal clashes
8 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.738 kcal/mol/HA) ✓ Good fit quality (FQ -7.19) ✓ Good H-bonds (4 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Very high strain energy (30.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-22.878
kcal/mol
LE
-0.738
kcal/mol/HA
Fit Quality
-7.19
FQ (Leeson)
HAC
31
heavy atoms
MW
440
Da
LogP
2.46
cLogP
Strain ΔE
30.7 kcal/mol
SASA buried
82%
Lipo contact
79% BSA apolar/total
SASA unbound
729 Ų
Apolar buried
475 Ų

Interaction summary

HB 4 HY 19 PI 0 CLASH 0
Final rank1.965Score-22.878
Inter norm-0.712Intra norm-0.026
Top1000noExcludedno
Contacts18H-bonds4
Artifact reasongeometry warning; 8 clashes; 1 protein clash; high strain Δ 30.7
Residues
ARG22 ARG342 ASN20 CYS26 GLN341 GLU343 GLU384 LEU25 LEU339 LEU372 LEU382 PRO338 PRO340 PRO344 PRO373 THR21 THR285 TYR370

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

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 overlap9Native recall0.60
Jaccard0.38RMSD-
HB strict1Strict recall0.17
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
488 1.1350204837366145 -0.70632 -22.4599 3 15 0 0.00 0.00 - no Open
464 1.9650560186041406 -0.711854 -22.8777 4 18 9 0.60 0.40 - no Current
428 3.160047468847212 -1.04503 -31.9693 7 13 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 -22.878kcal/mol
Ligand efficiency (LE) -0.7380kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.190
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 440.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.46
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 63.10kcal/mol
Minimised FF energy 32.42kcal/mol

SASA & burial

✓ computed
SASA (unbound) 728.6Ų
Total solvent-accessible surface area of free ligand
BSA total 599.6Ų
Buried surface area upon binding
BSA apolar 474.6Ų
Hydrophobic contacts buried
BSA polar 125.0Ų
Polar contacts buried
Fraction buried 82.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2530.8Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1376.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)