FAIRMol

Z31703705

Pose ID 9209 Compound 4085 Pose 401

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 Z31703705
PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
42.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.32, H-bond role recall 0.20
Burial
81%
Hydrophobic fit
81%
Reason: strain 42.8 kcal/mol
strain ΔE 42.8 kcal/mol 1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.730 kcal/mol/HA) ✓ Good fit quality (FQ -6.97) ✓ Good H-bonds (3 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Extreme strain energy (42.8 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Many internal clashes (11)
Score
-21.170
kcal/mol
LE
-0.730
kcal/mol/HA
Fit Quality
-6.97
FQ (Leeson)
HAC
29
heavy atoms
MW
487
Da
LogP
5.80
cLogP
Strain ΔE
42.8 kcal/mol
SASA buried
81%
Lipo contact
81% BSA apolar/total
SASA unbound
692 Ų
Apolar buried
450 Ų

Interaction summary

HB 3 HY 24 PI 0 CLASH 1

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
Final rank0.774Score-21.170
Inter norm-0.850Intra norm0.120
Top1000noExcludedno
Contacts18H-bonds3
Artifact reasongeometry warning; 11 clashes; 2 protein contact clashes; high strain Δ 42.8
Residues
ARG22 ARG342 CYS26 GLN341 GLU343 LEU25 LEU339 LEU350 LEU372 LEU382 PRO338 PRO340 PRO344 PRO373 THR21 THR285 TYR370 TYR371

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 overlap8Native recall0.53
Jaccard0.32RMSD-
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
401 0.7741397286888331 -0.849597 -21.1703 3 18 8 0.53 0.20 - no Current
411 1.4911761889571216 -0.645119 -19.8697 3 11 0 0.00 0.00 - no Open
477 3.7439465334665742 -0.820888 -24.7691 5 9 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 -21.170kcal/mol
Ligand efficiency (LE) -0.7300kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.968
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 487.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.80
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 42.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 72.99kcal/mol
Minimised FF energy 30.21kcal/mol

SASA & burial

✓ computed
SASA (unbound) 691.6Ų
Total solvent-accessible surface area of free ligand
BSA total 558.0Ų
Buried surface area upon binding
BSA apolar 450.1Ų
Hydrophobic contacts buried
BSA polar 107.9Ų
Polar contacts buried
Fraction buried 80.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2506.8Ų
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 1394.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)