FAIRMol

Z57108748

Pose ID 9225 Compound 2676 Pose 417

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 Z57108748
PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native mixed SASA done
Strain ΔE
16.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.47, Jaccard 0.33, H-bond role recall 0.20
Burial
83%
Hydrophobic fit
73%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.154 kcal/mol/HA) ✓ Good fit quality (FQ -9.46) ✓ Good H-bonds (5 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ Moderate strain (16.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-21.922
kcal/mol
LE
-1.154
kcal/mol/HA
Fit Quality
-9.46
FQ (Leeson)
HAC
19
heavy atoms
MW
254
Da
LogP
2.87
cLogP
Strain ΔE
16.5 kcal/mol
SASA buried
83%
Lipo contact
73% BSA apolar/total
SASA unbound
460 Ų
Apolar buried
279 Ų

Interaction summary

HB 5 HY 8 PI 0 CLASH 2
Final rank2.871Score-21.922
Inter norm-1.331Intra norm0.176
Top1000noExcludedno
Contacts13H-bonds5
Artifact reasongeometry warning; 9 clashes; 2 protein clashes
Residues
ARG337 ASP243 ASP385 GLU384 LEU339 LEU382 MET386 PHE326 PHE383 PRO338 THR241 VAL335 VAL336

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 overlap7Native recall0.47
Jaccard0.33RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
385 -0.23094152859741754 -1.72071 -30.2969 8 12 0 0.00 0.00 - no Open
395 2.6689546735600196 -1.42954 -24.9999 6 16 0 0.00 0.00 - no Open
417 2.870564801938861 -1.33148 -21.9216 5 13 7 0.47 0.20 - 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 -21.922kcal/mol
Ligand efficiency (LE) -1.1538kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.457
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 254.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.87
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 72.88kcal/mol
Minimised FF energy 56.34kcal/mol

SASA & burial

✓ computed
SASA (unbound) 460.2Ų
Total solvent-accessible surface area of free ligand
BSA total 383.3Ų
Buried surface area upon binding
BSA apolar 279.0Ų
Hydrophobic contacts buried
BSA polar 104.4Ų
Polar contacts buried
Fraction buried 83.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2323.4Ų
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 1373.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)