FAIRMol

Z19656164

Pose ID 9391 Compound 2146 Pose 583

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 Z19656164
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
16.0 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.47, Jaccard 0.39, H-bond role recall 0.20
Burial
73%
Hydrophobic fit
58%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 54% of hydrophobic surface appears solvent-exposed (7/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.072 kcal/mol/HA) ✓ Good fit quality (FQ -9.31) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (73% SASA buried) ✗ Moderate strain (16.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-23.583
kcal/mol
LE
-1.072
kcal/mol/HA
Fit Quality
-9.31
FQ (Leeson)
HAC
22
heavy atoms
MW
316
Da
LogP
1.69
cLogP
Strain ΔE
16.0 kcal/mol
SASA buried
73%
Lipo contact
58% BSA apolar/total
SASA unbound
544 Ų
Apolar buried
229 Ų

Interaction summary

HB 6 HY 5 PI 0 CLASH 4 ⚠ Exposure 53%
⚠️Partial hydrophobic solvent exposure
54% of hydrophobic surface appears solvent-exposed (7/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 13 Buried (contacted) 6 Exposed 7 LogP 1.69 H-bonds 6
Exposed fragments: phenyl (3/5 atoms exposed)phenyl (1/5 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank3.375Score-23.583
Inter norm-1.005Intra norm-0.067
Top1000noExcludedno
Contacts10H-bonds6
Artifact reasongeometry warning; 7 clashes; 2 protein clashes
Residues
ARG242 ARG337 ASP243 ASP385 GLU384 LEU339 PHE383 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
Jaccard0.39RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
583 2.1867385428156263 -1.35233 -25.5758 7 14 0 0.00 0.00 - no Open
583 3.374781540718053 -1.00537 -23.5826 6 10 7 0.47 0.20 - no Current
591 3.5277280153843713 -1.35116 -31.7001 12 14 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 -23.583kcal/mol
Ligand efficiency (LE) -1.0719kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.306
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 316.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.69
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 20.07kcal/mol
Minimised FF energy 4.06kcal/mol

SASA & burial

✓ computed
SASA (unbound) 543.6Ų
Total solvent-accessible surface area of free ligand
BSA total 394.8Ų
Buried surface area upon binding
BSA apolar 228.9Ų
Hydrophobic contacts buried
BSA polar 165.8Ų
Polar contacts buried
Fraction buried 72.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 58.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2299.7Ų
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 1394.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)