FAIRMol

Z56071437

Pose ID 5313 Compound 311 Pose 572

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
T08
T. brucei PTR1 T. brucei
Ligand Z56071437
PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
24.1 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.74, Jaccard 0.67, H-bond role recall 0.40
Burial
80%
Hydrophobic fit
78%
Reason: no major geometry red flags detected
1 protein-contact clashes 3 intramolecular clashes 38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.213 kcal/mol/HA) ✓ Good fit quality (FQ -11.82) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ High strain energy (24.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-37.599
kcal/mol
LE
-1.213
kcal/mol/HA
Fit Quality
-11.82
FQ (Leeson)
HAC
31
heavy atoms
MW
500
Da
LogP
5.50
cLogP
Strain ΔE
24.1 kcal/mol
SASA buried
80%
Lipo contact
78% BSA apolar/total
SASA unbound
753 Ų
Apolar buried
476 Ų

Interaction summary

HB 7 HY 24 PI 5 CLASH 3 ⚠ Exposure 38%

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
⚠️Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21 Buried (contacted) 13 Exposed 8 LogP 5.5 H-bonds 7
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank0.587Score-37.599
Inter norm-1.108Intra norm-0.105
Top1000noExcludedno
Contacts16H-bonds7
Artifact reasongeometry warning; 14 clashes; 1 protein contact clash; 1 severe cofactor-context clash; moderate strain Δ 24.1
Residues
ARG14 CYS168 LEU208 LEU209 LYS13 MET213 NAP301 PHE171 PHE97 PRO210 SER207 SER95 TRP221 TYR174 VAL206 VAL211

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap14Native recall0.74
Jaccard0.67RMSD-
HB strict3Strict recall0.50
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

Protein summary

258 residues
Protein targetT08Atoms3881
Residues258Chains2
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

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:NAP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
572 0.5870117947832066 -1.10765 -37.5989 7 16 14 0.74 0.40 - no Current
583 0.8823549273857154 -0.910836 -30.2227 2 20 0 0.00 0.00 - no Open
592 1.310495564240597 -0.754262 -27.3292 4 16 0 0.00 0.00 - no Open
611 1.7798849023795245 -0.802683 -26.2147 4 16 0 0.00 0.00 - no Open
594 1.9412230667148331 -0.877204 -32.0703 1 19 0 0.00 0.00 - no Open
584 2.0822003114507757 -0.856641 -25.7246 2 18 0 0.00 0.00 - no Open
583 2.606119674997513 -0.894636 -26.6402 9 16 0 0.00 0.00 - no Open
600 2.62217074979796 -0.689693 -24.6956 3 8 0 0.00 0.00 - no Open
575 3.3580502961066707 -0.8137 -25.6478 3 15 0 0.00 0.00 - no Open
595 3.5009994029016003 -0.774293 -24.4273 4 21 0 0.00 0.00 - no Open
587 3.744243536944524 -0.642671 -23.6962 5 10 0 0.00 0.00 - no Open
600 3.987159201366124 -1.08362 -33.2245 13 19 0 0.00 0.00 - no Open
591 6.027892840267617 -0.912188 -27.1412 8 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 -37.599kcal/mol
Ligand efficiency (LE) -1.2129kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.816
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 500.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.50
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -35.18kcal/mol
Minimised FF energy -59.33kcal/mol

SASA & burial

✓ computed
SASA (unbound) 753.3Ų
Total solvent-accessible surface area of free ligand
BSA total 606.6Ų
Buried surface area upon binding
BSA apolar 476.5Ų
Hydrophobic contacts buried
BSA polar 130.1Ų
Polar contacts buried
Fraction buried 80.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1724.9Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 941.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)