FAIRMol

Z55694322

Pose ID 2653 Compound 256 Pose 620

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
T04
L. major PTR1 L. major
Ligand Z55694322
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
41.8 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.74, Jaccard 0.70, H-bond role recall 0.00
Burial
81%
Hydrophobic fit
84%
Reason: no major geometry red flags detected
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.701 kcal/mol/HA) ✓ Good fit quality (FQ -6.96) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Extreme strain energy (41.8 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-23.131
kcal/mol
LE
-0.701
kcal/mol/HA
Fit Quality
-6.96
FQ (Leeson)
HAC
33
heavy atoms
MW
460
Da
LogP
5.10
cLogP
Strain ΔE
41.8 kcal/mol
SASA buried
81%
Lipo contact
84% BSA apolar/total
SASA unbound
732 Ų
Apolar buried
495 Ų

Interaction summary

HB 0 HY 24 PI 5 CLASH 1

HB · H-bonds
No hb · h-bonds detected for this pose.

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 rank0.912Score-23.131
Inter norm-0.743Intra norm0.042
Top1000noExcludedno
Contacts15H-bonds0
Artifact reasongeometry warning; 15 clashes; 1 cofactor-context clash; high strain Δ 41.5
Residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 MET233 NDP302 PHE113 SER111 SER227 TYR191 TYR194 VAL237 ARG287

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name7PXXContacts19
PoseOpen native poseHB0
IFP residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER112 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap14Native recall0.74
Jaccard0.70RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

308 residues
Protein targetT04Atoms4210
Residues308Chains3
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

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:NDP302

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
620 0.9124878828115518 -0.742763 -23.1308 0 15 14 0.74 0.00 - no Current
616 1.5903297613763936 -0.695296 -20.3004 1 17 0 0.00 0.00 - no Open
617 1.6999776302048877 -0.781972 -26.1696 4 14 0 0.00 0.00 - no Open
606 2.1579267805035065 -0.935582 -30.0151 4 17 0 0.00 0.00 - no Open
619 2.321598553519423 -0.843726 -27.1331 2 17 0 0.00 0.00 - no Open
611 2.3721997365242466 -0.744991 -19.006 2 19 0 0.00 0.00 - no Open
632 2.5845937659195366 -0.808096 -24.1504 9 17 0 0.00 0.00 - no Open
628 3.0667722052197655 -0.693175 -22.2941 6 15 0 0.00 0.00 - no Open
615 3.648743788972634 -0.72495 -21.5538 6 19 0 0.00 0.00 - no Open
629 4.069678458429272 -0.67542 -22.0358 6 19 0 0.00 0.00 - no Open
630 4.138721914791422 -0.806706 -25.3439 5 18 0 0.00 0.00 - no Open
616 5.015225112007658 -0.909212 -28.7073 9 17 0 0.00 0.00 - no Open
641 5.605204418092712 -1.11254 -33.8589 9 20 0 0.00 0.00 - no Open
631 5.82846986775583 -0.854024 -26.3807 7 19 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 -23.131kcal/mol
Ligand efficiency (LE) -0.7009kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.955
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 459.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.10
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 41.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 106.08kcal/mol
Minimised FF energy 64.29kcal/mol

SASA & burial

✓ computed
SASA (unbound) 731.9Ų
Total solvent-accessible surface area of free ligand
BSA total 591.9Ų
Buried surface area upon binding
BSA apolar 495.1Ų
Hydrophobic contacts buried
BSA polar 96.8Ų
Polar contacts buried
Fraction buried 80.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1754.7Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1044.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)