FAIRMol

Z1521553711

Pose ID 8518 Compound 1387 Pose 388

DB fairmolDocking 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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand Z1521553711
PDB1F3T↗

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 strong SASA done
Strain ΔE
13.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.79, Jaccard 0.75, H-bond role recall 0.57
Burial
80%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.311 kcal/mol/HA) ✓ Good fit quality (FQ -11.18) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Moderate strain (13.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-27.529
kcal/mol
LE
-1.311
kcal/mol/HA
Fit Quality
-11.18
FQ (Leeson)
HAC
21
heavy atoms
MW
307
Da
LogP
1.71
cLogP
Strain ΔE
13.2 kcal/mol
SASA buried
80%
Lipo contact
79% BSA apolar/total
SASA unbound
509 Ų
Apolar buried
321 Ų

Interaction summary

HB 8 HY 1 PI 3 CLASH 3

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

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank2.322Score-27.529
Inter norm-1.439Intra norm0.128
Top1000noExcludedno
Contacts16H-bonds8
Artifact reasongeometry warning; 9 clashes; 1 protein clash
Residues
ALA67 ARG154 ARG277 ASP332 ASP88 GLU274 GLY236 GLY237 GLY276 HIS197 HIS333 LYS69 PRO275 SER200 TYR331 TYR389

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap15Native recall0.79
Jaccard0.75RMSD-
HB strict4Strict recall0.44
HB same residue+role4HB role recall0.57
HB same residue5HB residue recall0.71

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
418 1.706034983384381 -1.42669 -24.5139 8 15 0 0.00 0.00 - no Open
388 2.3216341406732472 -1.43894 -27.529 8 16 15 0.79 0.57 - no Current
451 3.2126587318185202 -1.1889 -20.8917 6 14 0 0.00 0.00 - no Open
434 3.2709996425598846 -1.27088 -24.6443 8 14 0 0.00 0.00 - no Open
410 3.976349501105721 -1.3018 -24.3757 6 17 0 0.00 0.00 - no Open
387 4.466629566632373 -1.1529 -22.7938 7 17 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 -27.529kcal/mol
Ligand efficiency (LE) -1.3109kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.182
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 306.8Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.71
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 100.75kcal/mol
Minimised FF energy 87.55kcal/mol

SASA & burial

✓ computed
SASA (unbound) 509.1Ų
Total solvent-accessible surface area of free ligand
BSA total 404.9Ų
Buried surface area upon binding
BSA apolar 321.1Ų
Hydrophobic contacts buried
BSA polar 83.8Ų
Polar contacts buried
Fraction buried 79.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2494.8Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1387.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)