FAIRMol

Z19652710

Pose ID 9296 Compound 1854 Pose 488

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 Z19652710
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 medium Native mixed SASA done
Strain ΔE
5.2 kcal/mol
Protein clashes
4
Internal clashes
3
Native overlap
contact recall 0.40, Jaccard 0.30, H-bond role recall 0.20
Burial
81%
Hydrophobic fit
65%
Reason: no major geometry red flags detected
4 protein-contact clashes 3 intramolecular clashes 38% of hydrophobic surface appears solvent-exposed (5/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (5.2 kcal/mol) ✓ Excellent LE (-1.056 kcal/mol/HA) ✓ Good fit quality (FQ -8.83) ✓ Good H-bonds (5 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Geometry warnings ✗ Minor protein-contact clashes (4)
Score
-21.111
kcal/mol
LE
-1.056
kcal/mol/HA
Fit Quality
-8.83
FQ (Leeson)
HAC
20
heavy atoms
MW
305
Da
LogP
3.32
cLogP
Strain ΔE
5.2 kcal/mol
SASA buried
81%
Lipo contact
65% BSA apolar/total
SASA unbound
535 Ų
Apolar buried
284 Ų

Interaction summary

HB 5 HY 8 PI 0 CLASH 0 ⚠ Exposure 38%

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.
⚠️Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (5/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 13 Buried (contacted) 8 Exposed 5 LogP 3.32 H-bonds 5
Exposed fragments: phenyl (3/5 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank0.077Score-21.111
Inter norm-1.098Intra norm0.043
Top1000noExcludedno
Contacts11H-bonds5
Artifact reasongeometry warning; 3 clashes; 4 protein contact clashes
Residues
ARG22 ARG342 ASN20 CYS26 GLN341 GLU343 LEU25 LEU382 PRO340 THR21 THR285

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 strict1Strict recall0.17
HB same residue+role1HB role recall0.20
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
488 0.07748725599830515 -1.09846 -21.111 5 11 6 0.40 0.20 - no Current
517 0.29968302526280177 -1.03568 -19.5522 4 11 0 0.00 0.00 - no Open
485 1.8038394012921375 -1.30437 -26.1579 3 11 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 -21.111kcal/mol
Ligand efficiency (LE) -1.0555kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.833
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 305.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.32
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 5.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -8.29kcal/mol
Minimised FF energy -13.50kcal/mol

SASA & burial

✓ computed
SASA (unbound) 534.6Ų
Total solvent-accessible surface area of free ligand
BSA total 434.5Ų
Buried surface area upon binding
BSA apolar 284.1Ų
Hydrophobic contacts buried
BSA polar 150.4Ų
Polar contacts buried
Fraction buried 81.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2334.1Ų
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 1379.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)